[med-svn] r329 - in trunk/packages/gbrowse/trunk: . bin conf conf/MobyServices debian debian/patches libalign
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Fri Jun 15 00:07:47 UTC 2007
Author: charles-guest
Date: 2007-06-15 00:07:47 +0000 (Fri, 15 Jun 2007)
New Revision: 329
Added:
trunk/packages/gbrowse/trunk/GGB.def
trunk/packages/gbrowse/trunk/Makefile.old
trunk/packages/gbrowse/trunk/bin/
trunk/packages/gbrowse/trunk/bin/load_genbank.pl
trunk/packages/gbrowse/trunk/bin/make_das_conf.pl
trunk/packages/gbrowse/trunk/bin/process_gadfly.pl
trunk/packages/gbrowse/trunk/bin/process_sgd.pl
trunk/packages/gbrowse/trunk/bin/process_wormbase.pl
trunk/packages/gbrowse/trunk/bin/register_moby_services.pl
trunk/packages/gbrowse/trunk/bin/ucsc_genes2gff.pl
trunk/packages/gbrowse/trunk/conf/
trunk/packages/gbrowse/trunk/conf/MobyServices/
trunk/packages/gbrowse/trunk/conf/MobyServices/GbrowseServices.pm
trunk/packages/gbrowse/trunk/debian/
trunk/packages/gbrowse/trunk/debian/README.Debian
trunk/packages/gbrowse/trunk/debian/changelog
trunk/packages/gbrowse/trunk/debian/compat
trunk/packages/gbrowse/trunk/debian/control
trunk/packages/gbrowse/trunk/debian/copyright
trunk/packages/gbrowse/trunk/debian/dirs
trunk/packages/gbrowse/trunk/debian/docs
trunk/packages/gbrowse/trunk/debian/generic-genome-browser.doc-base.EX
trunk/packages/gbrowse/trunk/debian/patches/
trunk/packages/gbrowse/trunk/debian/patches/10_usrlocalperl.patch
trunk/packages/gbrowse/trunk/debian/patches/series
trunk/packages/gbrowse/trunk/debian/rules
trunk/packages/gbrowse/trunk/debian/watch.ex
trunk/packages/gbrowse/trunk/libalign/
trunk/packages/gbrowse/trunk/libalign/Makefile.old
trunk/packages/gbrowse/trunk/pod2htmd.tmp
trunk/packages/gbrowse/trunk/pod2htmi.tmp
Log:
[svn-inject] Applying Debian modifications to trunk
Added: trunk/packages/gbrowse/trunk/GGB.def
===================================================================
--- trunk/packages/gbrowse/trunk/GGB.def (rev 0)
+++ trunk/packages/gbrowse/trunk/GGB.def 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,11 @@
+# This hints file contains configuration information used by the generic browser
+
+# To reconfigure, run perl Makefile.PL `cat GGB.def`
+
+CGIBIN=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse/usr/lib/cgi-bin
+DO_XS=1
+APACHE=/usr/local/apache
+CONF=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse/etc/
+HTDOCS=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse/var/www
+VERSION=1.68
+BIOGRAPHICS_VERSION=1.654
Added: trunk/packages/gbrowse/trunk/Makefile.old
===================================================================
--- trunk/packages/gbrowse/trunk/Makefile.old (rev 0)
+++ trunk/packages/gbrowse/trunk/Makefile.old 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,1392 @@
+# This Makefile is for the Generic-Genome-Browser extension to perl.
+#
+# It was generated automatically by MakeMaker version
+# 6.30_01 (Revision: Revision: 4535 ) from the contents of
+# Makefile.PL. Don't edit this file, edit Makefile.PL instead.
+#
+# ANY CHANGES MADE HERE WILL BE LOST!
+#
+# MakeMaker ARGV: (q[DESTDIR=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse], q[INSTALLDIRS=vendor], q[VENDORARCHEXP=/usr/share/perl5])
+#
+# MakeMaker Parameters:
+
+# ABSTRACT => q[A CGI-driven browser for genomic annotations.]
+# AUTHOR => q[Lincoln Stein (lstein at cshl.org)]
+# DEFINE => q[]
+# DIR => [q[libalign]]
+# EXE_FILES => [q[bin/register_moby_services.pl], q[bin/make_das_conf.pl], q[bin/process_wormbase.pl], q[bin/process_sgd.pl], q[bin/process_gadfly.pl], q[bin/load_genbank.pl]]
+# INC => q[]
+# INSTALLSCRIPT => undef
+# INSTALLSITEMAN1DIR => undef
+# INSTALLSITEMAN3DIR => undef
+# LIB => undef
+# LIBS => [q[]]
+# NAME => q[Generic-Genome-Browser]
+# PL_FILES => { install_util/gbrowse_ppm_install.PLS=>q[install_util/gbrowse_ppm_install.pl], bin/load_genbank.PLS=>q[bin/load_genbank.pl], install_util/conf_install.PLS=>q[install_util/conf_install.pl], bin/process_sgd.PLS=>q[bin/process_sgd.pl], bin/ucsc_genes2gff.PLS=>q[bin/ucsc_genes2gff.pl], bin/process_wormbase.PLS=>q[bin/process_wormbase.pl], bin/make_das_conf.PLS=>q[bin/make_das_conf.pl], bin/process_gadfly.PLS=>q[bin/process_gadfly.pl], cgi-bin/gbrowse.PLS=>q[cgi-bin/gbrowse], cgi-bin/gbrowse_img.PLS=>q[cgi-bin/gbrowse_img], install_util/htdocs_install.PLS=>q[install_util/htdocs_install.pl], bin/register_moby_services.PLS=>q[bin/register_moby_services.pl], install_util/cgi_install.PLS=>q[install_util/cgi_install.pl], cgi-bin/gbrowse_moby.PLS=>q[cgi-bin/gbrowse_moby], cgi-bin/gbrowse_details.PLS=>q[cgi-bin/gbrowse_details], cgi-bin/das.PLS=>q[cgi-bin/das], cgi-bin/moby_server.PLS=>q[cgi-bin/moby_server], conf/MobyServices/GbrowseServices.PMS=>q[conf/MobyServices/GbrowseServices.pm], cgi-bin/gbrowse_est.PLS=>q[cgi-bin/gbrowse_est] }
+# PREREQ_PM => { Class::Base=>q[0], IO::String=>q[0], Text::Shellwords=>q[1.08], Bio::Perl=>q[1.005002], CGI::Session=>q[4.02], File::Temp=>q[0], Digest::MD5=>q[0], GD=>q[2.07] }
+# VERSION => q[1.68]
+
+# --- MakeMaker post_initialize section:
+
+
+# --- MakeMaker const_config section:
+
+# These definitions are from config.sh (via /usr/lib/perl/5.8/Config.pm)
+
+# They may have been overridden via Makefile.PL or on the command line
+AR = ar
+CC = cc
+CCCDLFLAGS = -fPIC
+CCDLFLAGS = -Wl,-E
+DLEXT = so
+DLSRC = dl_dlopen.xs
+LD = cc
+LDDLFLAGS = -shared -L/usr/local/lib
+LDFLAGS = -L/usr/local/lib
+LIBC = /lib/libc-2.3.6.so
+LIB_EXT = .a
+OBJ_EXT = .o
+OSNAME = linux
+OSVERS = 2.6.8-powerpc-smp
+RANLIB = :
+SITELIBEXP = /usr/local/share/perl/5.8.8
+SITEARCHEXP = /usr/local/lib/perl/5.8.8
+SO = so
+EXE_EXT =
+FULL_AR = /usr/bin/ar
+VENDORARCHEXP = /usr/share/perl5
+VENDORLIBEXP = /usr/share/perl5
+
+
+# --- MakeMaker constants section:
+AR_STATIC_ARGS = cr
+DIRFILESEP = /
+DFSEP = $(DIRFILESEP)
+NAME = Generic-Genome-Browser
+NAME_SYM = Generic_Genome_Browser
+VERSION = 1.68
+VERSION_MACRO = VERSION
+VERSION_SYM = 1_68
+DEFINE_VERSION = -D$(VERSION_MACRO)=\"$(VERSION)\"
+XS_VERSION = 1.68
+XS_VERSION_MACRO = XS_VERSION
+XS_DEFINE_VERSION = -D$(XS_VERSION_MACRO)=\"$(XS_VERSION)\"
+INST_ARCHLIB = blib/arch
+INST_SCRIPT = blib/script
+INST_BIN = blib/bin
+INST_LIB = blib/lib
+INST_MAN1DIR = blib/man1
+INST_MAN3DIR = blib/man3
+MAN1EXT = 1p
+MAN3EXT = 3pm
+INSTALLDIRS = vendor
+DESTDIR = /tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse
+PREFIX = /usr
+PERLPREFIX = $(PREFIX)
+SITEPREFIX = $(PREFIX)/local
+VENDORPREFIX = $(PREFIX)
+INSTALLPRIVLIB = $(PERLPREFIX)/share/perl/5.8
+DESTINSTALLPRIVLIB = $(DESTDIR)$(INSTALLPRIVLIB)
+INSTALLSITELIB = $(SITEPREFIX)/share/perl/5.8.8
+DESTINSTALLSITELIB = $(DESTDIR)$(INSTALLSITELIB)
+INSTALLVENDORLIB = $(VENDORPREFIX)/share/perl5
+DESTINSTALLVENDORLIB = $(DESTDIR)$(INSTALLVENDORLIB)
+INSTALLARCHLIB = $(PERLPREFIX)/lib/perl/5.8
+DESTINSTALLARCHLIB = $(DESTDIR)$(INSTALLARCHLIB)
+INSTALLSITEARCH = $(SITEPREFIX)/lib/perl/5.8.8
+DESTINSTALLSITEARCH = $(DESTDIR)$(INSTALLSITEARCH)
+INSTALLVENDORARCH = $(VENDORPREFIX)/lib/perl5
+DESTINSTALLVENDORARCH = $(DESTDIR)$(INSTALLVENDORARCH)
+INSTALLBIN = $(PERLPREFIX)/bin
+DESTINSTALLBIN = $(DESTDIR)$(INSTALLBIN)
+INSTALLSITEBIN = $(SITEPREFIX)/bin
+DESTINSTALLSITEBIN = $(DESTDIR)$(INSTALLSITEBIN)
+INSTALLVENDORBIN = $(VENDORPREFIX)/bin
+DESTINSTALLVENDORBIN = $(DESTDIR)$(INSTALLVENDORBIN)
+INSTALLSCRIPT = $(PERLPREFIX)/bin
+DESTINSTALLSCRIPT = $(DESTDIR)$(INSTALLSCRIPT)
+INSTALLSITESCRIPT = $(SITEPREFIX)/bin
+DESTINSTALLSITESCRIPT = $(DESTDIR)$(INSTALLSITESCRIPT)
+INSTALLVENDORSCRIPT = $(VENDORPREFIX)/bin
+DESTINSTALLVENDORSCRIPT = $(DESTDIR)$(INSTALLVENDORSCRIPT)
+INSTALLMAN1DIR = $(PERLPREFIX)/share/man/man1
+DESTINSTALLMAN1DIR = $(DESTDIR)$(INSTALLMAN1DIR)
+INSTALLSITEMAN1DIR = $(SITEPREFIX)/man/man1
+DESTINSTALLSITEMAN1DIR = $(DESTDIR)$(INSTALLSITEMAN1DIR)
+INSTALLVENDORMAN1DIR = $(VENDORPREFIX)/share/man/man1
+DESTINSTALLVENDORMAN1DIR = $(DESTDIR)$(INSTALLVENDORMAN1DIR)
+INSTALLMAN3DIR = $(PERLPREFIX)/share/man/man3
+DESTINSTALLMAN3DIR = $(DESTDIR)$(INSTALLMAN3DIR)
+INSTALLSITEMAN3DIR = $(SITEPREFIX)/man/man3
+DESTINSTALLSITEMAN3DIR = $(DESTDIR)$(INSTALLSITEMAN3DIR)
+INSTALLVENDORMAN3DIR = $(VENDORPREFIX)/share/man/man3
+DESTINSTALLVENDORMAN3DIR = $(DESTDIR)$(INSTALLVENDORMAN3DIR)
+PERL_LIB = /usr/share/perl/5.8
+PERL_ARCHLIB = /usr/lib/perl/5.8
+LIBPERL_A = libperl.a
+FIRST_MAKEFILE = Makefile
+MAKEFILE_OLD = Makefile.old
+MAKE_APERL_FILE = Makefile.aperl
+PERLMAINCC = $(CC)
+PERL_INC = /usr/lib/perl/5.8/CORE
+PERL = /usr/bin/perl
+FULLPERL = /usr/bin/perl
+ABSPERL = $(PERL)
+PERLRUN = $(PERL)
+FULLPERLRUN = $(FULLPERL)
+ABSPERLRUN = $(ABSPERL)
+PERLRUNINST = $(PERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
+FULLPERLRUNINST = $(FULLPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
+ABSPERLRUNINST = $(ABSPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
+PERL_CORE = 0
+PERM_RW = 644
+PERM_RWX = 755
+
+MAKEMAKER = /usr/share/perl/5.8/ExtUtils/MakeMaker.pm
+MM_VERSION = 6.30_01
+MM_REVISION = Revision: 4535
+
+# FULLEXT = Pathname for extension directory (eg Foo/Bar/Oracle).
+# BASEEXT = Basename part of FULLEXT. May be just equal FULLEXT. (eg Oracle)
+# PARENT_NAME = NAME without BASEEXT and no trailing :: (eg Foo::Bar)
+# DLBASE = Basename part of dynamic library. May be just equal BASEEXT.
+FULLEXT = Generic-Genome-Browser
+BASEEXT = Browser
+PARENT_NAME =
+DLBASE = $(BASEEXT)
+VERSION_FROM =
+INC =
+DEFINE =
+OBJECT =
+LDFROM = $(OBJECT)
+LINKTYPE = dynamic
+BOOTDEP =
+
+# Handy lists of source code files:
+XS_FILES =
+C_FILES =
+O_FILES =
+H_FILES =
+MAN1PODS = bin/load_genbank.pl \
+ bin/make_das_conf.pl \
+ bin/process_gadfly.pl \
+ bin/process_sgd.pl \
+ bin/process_wormbase.pl
+MAN3PODS = lib/Bio/DB/Das/BioSQL.pm \
+ lib/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm \
+ lib/Bio/DB/Das/BioSQL/DBAdaptor.pm \
+ lib/Bio/DB/Das/BioSQL/PartialSeqAdaptor.pm \
+ lib/Bio/DB/Das/BioSQL/Segment.pm \
+ lib/Bio/DB/Das/Chado.pm \
+ lib/Bio/DB/Das/Chado/Segment.pm \
+ lib/Bio/DB/Das/Chado/Segment/Feature.pm \
+ lib/Bio/DB/GFF/Aggregator/match_gap.pm \
+ lib/Bio/DB/GFF/Aggregator/orf.pm \
+ lib/Bio/DB/GFF/Aggregator/reftranscript.pm \
+ lib/Bio/DB/GFF/Aggregator/waba_alignment.pm \
+ lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm \
+ lib/Bio/Graphics/Browser.pm \
+ lib/Bio/Graphics/Browser/GFFhelper.pm \
+ lib/Bio/Graphics/Browser/Markup.pm \
+ lib/Bio/Graphics/Browser/PadAlignment.pm \
+ lib/Bio/Graphics/Browser/Plugin.pm \
+ lib/Bio/Graphics/Browser/PluginSet.pm \
+ lib/Bio/Graphics/Browser/Realign.pm \
+ lib/Bio/Graphics/Browser/RemoteSet.pm \
+ lib/Bio/Graphics/Browser/UploadSet.pm \
+ lib/Bio/Graphics/Browser/Util.pm \
+ lib/Bio/Graphics/FeatureFile.pm \
+ lib/Bio/Graphics/Glyph/allele_tower.pm \
+ lib/Bio/Graphics/Glyph/genscan_transcript.pm \
+ lib/Bio/Graphics/Glyph/heat_map.pm \
+ lib/Bio/Graphics/Glyph/heat_map_ideogram.pm \
+ lib/Bio/Graphics/Glyph/ideogram.pm \
+ lib/Bio/Graphics/Glyph/insertion_chromosome.pm \
+ lib/Bio/Graphics/Glyph/ld_plot.pm \
+ lib/Bio/Graphics/Glyph/pairwise_plot.pm \
+ lib/Bio/Graphics/Glyph/spectrogram.pm \
+ lib/Bio/Graphics/Glyph/trace.pm \
+ lib/Bio/Graphics/Glyph/wormbase_transcript.pm \
+ lib/CGI/Session/ID/salted_md5.pm \
+ lib/CGI/Toggle.pm
+
+# Where is the Config information that we are using/depend on
+CONFIGDEP = $(PERL_ARCHLIB)$(DFSEP)Config.pm $(PERL_INC)$(DFSEP)config.h
+
+# Where to build things
+INST_LIBDIR = $(INST_LIB)
+INST_ARCHLIBDIR = $(INST_ARCHLIB)
+
+INST_AUTODIR = $(INST_LIB)/auto/$(FULLEXT)
+INST_ARCHAUTODIR = $(INST_ARCHLIB)/auto/$(FULLEXT)
+
+INST_STATIC =
+INST_DYNAMIC =
+INST_BOOT =
+
+# Extra linker info
+EXPORT_LIST =
+PERL_ARCHIVE =
+PERL_ARCHIVE_AFTER =
+
+
+TO_INST_PM = lib/Bio/DB/Das/BioSQL.pm \
+ lib/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm \
+ lib/Bio/DB/Das/BioSQL/DBAdaptor.pm \
+ lib/Bio/DB/Das/BioSQL/Iterator.pm \
+ lib/Bio/DB/Das/BioSQL/PartialSeqAdaptor.pm \
+ lib/Bio/DB/Das/BioSQL/Segment.pm \
+ lib/Bio/DB/Das/Chado.pm \
+ lib/Bio/DB/Das/Chado/Segment.pm \
+ lib/Bio/DB/Das/Chado/Segment/Feature.pm \
+ lib/Bio/DB/GFF/Aggregator/match_gap.pm \
+ lib/Bio/DB/GFF/Aggregator/orf.pm \
+ lib/Bio/DB/GFF/Aggregator/reftranscript.pm \
+ lib/Bio/DB/GFF/Aggregator/waba_alignment.pm \
+ lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm \
+ lib/Bio/Graphics/Browser.pm \
+ lib/Bio/Graphics/Browser/GFFhelper.pm \
+ lib/Bio/Graphics/Browser/I18n.pm \
+ lib/Bio/Graphics/Browser/Markup.pm \
+ lib/Bio/Graphics/Browser/PadAlignment.pm \
+ lib/Bio/Graphics/Browser/PageSettings.pm \
+ lib/Bio/Graphics/Browser/Plugin.pm \
+ lib/Bio/Graphics/Browser/PluginSet.pm \
+ lib/Bio/Graphics/Browser/Realign.pm \
+ lib/Bio/Graphics/Browser/RemoteSet.pm \
+ lib/Bio/Graphics/Browser/UploadSet.pm \
+ lib/Bio/Graphics/Browser/Util.pm \
+ lib/Bio/Graphics/FeatureFile.pm \
+ lib/Bio/Graphics/Glyph/allele_tower.pm \
+ lib/Bio/Graphics/Glyph/connector.pm \
+ lib/Bio/Graphics/Glyph/drosophila_arrow.pm \
+ lib/Bio/Graphics/Glyph/genscan_transcript.pm \
+ lib/Bio/Graphics/Glyph/heat_map.pm \
+ lib/Bio/Graphics/Glyph/heat_map_ideogram.pm \
+ lib/Bio/Graphics/Glyph/ideogram.pm \
+ lib/Bio/Graphics/Glyph/insertion_chromosome.pm \
+ lib/Bio/Graphics/Glyph/ld_plot.pm \
+ lib/Bio/Graphics/Glyph/pairwise_plot.pm \
+ lib/Bio/Graphics/Glyph/phased_exons.pm \
+ lib/Bio/Graphics/Glyph/spectrogram.pm \
+ lib/Bio/Graphics/Glyph/trace.pm \
+ lib/Bio/Graphics/Glyph/wormbase_transcript.pm \
+ lib/CGI/Session/ID/salted_md5.pm \
+ lib/CGI/Toggle.pm
+
+PM_TO_BLIB = lib/Bio/Graphics/Glyph/trace.pm \
+ blib/lib/Bio/Graphics/Glyph/trace.pm \
+ lib/Bio/Graphics/Browser/I18n.pm \
+ blib/lib/Bio/Graphics/Browser/I18n.pm \
+ lib/Bio/Graphics/Browser/Plugin.pm \
+ blib/lib/Bio/Graphics/Browser/Plugin.pm \
+ lib/Bio/Graphics/Glyph/genscan_transcript.pm \
+ blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm \
+ lib/Bio/Graphics/Browser/Realign.pm \
+ blib/lib/Bio/Graphics/Browser/Realign.pm \
+ lib/Bio/Graphics/Glyph/wormbase_transcript.pm \
+ blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm \
+ lib/Bio/Graphics/FeatureFile.pm \
+ blib/lib/Bio/Graphics/FeatureFile.pm \
+ lib/Bio/DB/GFF/Aggregator/reftranscript.pm \
+ blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm \
+ lib/Bio/DB/Das/BioSQL/PartialSeqAdaptor.pm \
+ blib/lib/Bio/DB/Das/BioSQL/PartialSeqAdaptor.pm \
+ lib/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm \
+ blib/lib/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm \
+ lib/Bio/DB/Das/Chado/Segment/Feature.pm \
+ blib/lib/Bio/DB/Das/Chado/Segment/Feature.pm \
+ lib/Bio/Graphics/Glyph/ld_plot.pm \
+ blib/lib/Bio/Graphics/Glyph/ld_plot.pm \
+ lib/Bio/DB/GFF/Aggregator/waba_alignment.pm \
+ blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm \
+ lib/Bio/DB/GFF/Aggregator/orf.pm \
+ blib/lib/Bio/DB/GFF/Aggregator/orf.pm \
+ lib/Bio/Graphics/Glyph/drosophila_arrow.pm \
+ blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm \
+ lib/Bio/Graphics/Glyph/spectrogram.pm \
+ blib/lib/Bio/Graphics/Glyph/spectrogram.pm \
+ lib/Bio/Graphics/Browser/PadAlignment.pm \
+ blib/lib/Bio/Graphics/Browser/PadAlignment.pm \
+ lib/Bio/DB/Das/BioSQL/Iterator.pm \
+ blib/lib/Bio/DB/Das/BioSQL/Iterator.pm \
+ lib/Bio/DB/Das/BioSQL/DBAdaptor.pm \
+ blib/lib/Bio/DB/Das/BioSQL/DBAdaptor.pm \
+ lib/Bio/Graphics/Browser.pm \
+ blib/lib/Bio/Graphics/Browser.pm \
+ lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm \
+ blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm \
+ lib/Bio/Graphics/Glyph/ideogram.pm \
+ blib/lib/Bio/Graphics/Glyph/ideogram.pm \
+ lib/Bio/Graphics/Glyph/phased_exons.pm \
+ blib/lib/Bio/Graphics/Glyph/phased_exons.pm \
+ lib/Bio/DB/Das/BioSQL/Segment.pm \
+ blib/lib/Bio/DB/Das/BioSQL/Segment.pm \
+ lib/Bio/Graphics/Browser/PageSettings.pm \
+ blib/lib/Bio/Graphics/Browser/PageSettings.pm \
+ lib/Bio/Graphics/Browser/PluginSet.pm \
+ blib/lib/Bio/Graphics/Browser/PluginSet.pm \
+ lib/CGI/Session/ID/salted_md5.pm \
+ blib/lib/CGI/Session/ID/salted_md5.pm \
+ lib/Bio/DB/GFF/Aggregator/match_gap.pm \
+ blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm \
+ lib/Bio/Graphics/Glyph/heat_map.pm \
+ blib/lib/Bio/Graphics/Glyph/heat_map.pm \
+ lib/CGI/Toggle.pm \
+ blib/lib/CGI/Toggle.pm \
+ lib/Bio/Graphics/Browser/GFFhelper.pm \
+ blib/lib/Bio/Graphics/Browser/GFFhelper.pm \
+ lib/Bio/Graphics/Browser/RemoteSet.pm \
+ blib/lib/Bio/Graphics/Browser/RemoteSet.pm \
+ lib/Bio/Graphics/Glyph/insertion_chromosome.pm \
+ blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm \
+ lib/Bio/Graphics/Glyph/pairwise_plot.pm \
+ blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm \
+ lib/Bio/Graphics/Glyph/allele_tower.pm \
+ blib/lib/Bio/Graphics/Glyph/allele_tower.pm \
+ lib/Bio/Graphics/Browser/Util.pm \
+ blib/lib/Bio/Graphics/Browser/Util.pm \
+ lib/Bio/DB/Das/Chado.pm \
+ blib/lib/Bio/DB/Das/Chado.pm \
+ lib/Bio/Graphics/Browser/Markup.pm \
+ blib/lib/Bio/Graphics/Browser/Markup.pm \
+ lib/Bio/Graphics/Glyph/heat_map_ideogram.pm \
+ blib/lib/Bio/Graphics/Glyph/heat_map_ideogram.pm \
+ lib/Bio/DB/Das/BioSQL.pm \
+ blib/lib/Bio/DB/Das/BioSQL.pm \
+ lib/Bio/Graphics/Glyph/connector.pm \
+ blib/lib/Bio/Graphics/Glyph/connector.pm \
+ lib/Bio/DB/Das/Chado/Segment.pm \
+ blib/lib/Bio/DB/Das/Chado/Segment.pm \
+ lib/Bio/Graphics/Browser/UploadSet.pm \
+ blib/lib/Bio/Graphics/Browser/UploadSet.pm
+
+
+# --- MakeMaker platform_constants section:
+MM_Unix_VERSION = 1.50_01
+PERL_MALLOC_DEF = -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc
+
+
+# --- MakeMaker tool_autosplit section:
+# Usage: $(AUTOSPLITFILE) FileToSplit AutoDirToSplitInto
+AUTOSPLITFILE = $(ABSPERLRUN) -e 'use AutoSplit; autosplit($$ARGV[0], $$ARGV[1], 0, 1, 1)'
+
+
+
+# --- MakeMaker tool_xsubpp section:
+
+XSUBPPDIR = /usr/share/perl/5.8/ExtUtils
+XSUBPP = $(XSUBPPDIR)$(DFSEP)xsubpp
+XSUBPPRUN = $(PERLRUN) $(XSUBPP)
+XSPROTOARG =
+XSUBPPDEPS = /usr/share/perl/5.8/ExtUtils/typemap $(XSUBPP)
+XSUBPPARGS = -typemap /usr/share/perl/5.8/ExtUtils/typemap
+XSUBPP_EXTRA_ARGS =
+
+
+# --- MakeMaker tools_other section:
+SHELL = /bin/sh
+CHMOD = chmod
+CP = cp
+MV = mv
+NOOP = $(SHELL) -c true
+NOECHO = @
+RM_F = rm -f
+RM_RF = rm -rf
+TEST_F = test -f
+TOUCH = touch
+UMASK_NULL = umask 0
+DEV_NULL = > /dev/null 2>&1
+MKPATH = $(ABSPERLRUN) "-MExtUtils::Command" -e mkpath
+EQUALIZE_TIMESTAMP = $(ABSPERLRUN) "-MExtUtils::Command" -e eqtime
+ECHO = echo
+ECHO_N = echo -n
+UNINST = 0
+VERBINST = 0
+MOD_INSTALL = $(ABSPERLRUN) -MExtUtils::Install -e 'install({@ARGV}, '\''$(VERBINST)'\'', 0, '\''$(UNINST)'\'');'
+DOC_INSTALL = $(ABSPERLRUN) "-MExtUtils::Command::MM" -e perllocal_install
+UNINSTALL = $(ABSPERLRUN) "-MExtUtils::Command::MM" -e uninstall
+WARN_IF_OLD_PACKLIST = $(ABSPERLRUN) "-MExtUtils::Command::MM" -e warn_if_old_packlist
+MACROSTART =
+MACROEND =
+USEMAKEFILE = -f
+FIXIN = $(PERLRUN) "-MExtUtils::MY" -e "MY->fixin(shift)"
+
+
+# --- MakeMaker makemakerdflt section:
+makemakerdflt: all
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker dist section:
+TAR = tar
+TARFLAGS = cvf
+ZIP = zip
+ZIPFLAGS = -r
+COMPRESS = gzip --best
+SUFFIX = .gz
+SHAR = shar
+PREOP = $(NOECHO) $(NOOP)
+POSTOP = $(NOECHO) $(NOOP)
+TO_UNIX = $(NOECHO) $(NOOP)
+CI = ci -u
+RCS_LABEL = rcs -Nv$(VERSION_SYM): -q
+DIST_CP = best
+DIST_DEFAULT = tardist
+DISTNAME = Generic-Genome-Browser
+DISTVNAME = Generic-Genome-Browser-1.68
+
+
+# --- MakeMaker macro section:
+
+
+# --- MakeMaker depend section:
+
+
+# --- MakeMaker cflags section:
+
+CCFLAGS = -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBIAN -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
+OPTIMIZE = -O2
+PERLTYPE =
+MPOLLUTE =
+
+
+# --- MakeMaker const_loadlibs section:
+
+# Generic-Genome-Browser might depend on some other libraries:
+# See ExtUtils::Liblist for details
+#
+
+
+# --- MakeMaker const_cccmd section:
+CCCMD = $(CC) -c $(PASTHRU_INC) $(INC) \
+ $(CCFLAGS) $(OPTIMIZE) \
+ $(PERLTYPE) $(MPOLLUTE) $(DEFINE_VERSION) \
+ $(XS_DEFINE_VERSION)
+
+# --- MakeMaker post_constants section:
+
+
+# --- MakeMaker pasthru section:
+
+PASTHRU = LIBPERL_A="$(LIBPERL_A)"\
+ LINKTYPE="$(LINKTYPE)"\
+ OPTIMIZE="$(OPTIMIZE)"\
+ PREFIX="$(PREFIX)"\
+ PASTHRU_DEFINE="$(PASTHRU_DEFINE)"\
+ PASTHRU_INC="$(PASTHRU_INC)"
+
+
+# --- MakeMaker special_targets section:
+.SUFFIXES : .xs .c .C .cpp .i .s .cxx .cc $(OBJ_EXT)
+
+.PHONY: all config static dynamic test linkext manifest blibdirs clean realclean disttest distdir
+
+
+
+# --- MakeMaker c_o section:
+
+.c.i:
+ cc -E -c $(PASTHRU_INC) $(INC) \
+ $(CCFLAGS) $(OPTIMIZE) \
+ $(PERLTYPE) $(MPOLLUTE) $(DEFINE_VERSION) \
+ $(XS_DEFINE_VERSION) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c > $*.i
+
+.c.s:
+ $(CCCMD) -S $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c
+
+.c$(OBJ_EXT):
+ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c
+
+.C$(OBJ_EXT):
+ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.C
+
+.cpp$(OBJ_EXT):
+ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cpp
+
+.cxx$(OBJ_EXT):
+ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cxx
+
+.cc$(OBJ_EXT):
+ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cc
+
+
+# --- MakeMaker xs_c section:
+
+.xs.c:
+ $(XSUBPPRUN) $(XSPROTOARG) $(XSUBPPARGS) $(XSUBPP_EXTRA_ARGS) $*.xs > $*.xsc && $(MV) $*.xsc $*.c
+
+
+# --- MakeMaker xs_o section:
+
+.xs$(OBJ_EXT):
+ $(XSUBPPRUN) $(XSPROTOARG) $(XSUBPPARGS) $*.xs > $*.xsc && $(MV) $*.xsc $*.c
+ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c
+
+
+# --- MakeMaker top_targets section:
+all :: pure_all manifypods
+ $(NOECHO) $(NOOP)
+
+
+pure_all :: config pm_to_blib subdirs linkext
+ $(NOECHO) $(NOOP)
+
+subdirs :: $(MYEXTLIB)
+ $(NOECHO) $(NOOP)
+
+config :: $(FIRST_MAKEFILE) blibdirs
+ $(NOECHO) $(NOOP)
+
+help :
+ perldoc ExtUtils::MakeMaker
+
+
+# --- MakeMaker blibdirs section:
+blibdirs : $(INST_LIBDIR)$(DFSEP).exists $(INST_ARCHLIB)$(DFSEP).exists $(INST_AUTODIR)$(DFSEP).exists $(INST_ARCHAUTODIR)$(DFSEP).exists $(INST_BIN)$(DFSEP).exists $(INST_SCRIPT)$(DFSEP).exists $(INST_MAN1DIR)$(DFSEP).exists $(INST_MAN3DIR)$(DFSEP).exists
+ $(NOECHO) $(NOOP)
+
+# Backwards compat with 6.18 through 6.25
+blibdirs.ts : blibdirs
+ $(NOECHO) $(NOOP)
+
+$(INST_LIBDIR)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_LIBDIR)
+ $(NOECHO) $(CHMOD) 755 $(INST_LIBDIR)
+ $(NOECHO) $(TOUCH) $(INST_LIBDIR)$(DFSEP).exists
+
+$(INST_ARCHLIB)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_ARCHLIB)
+ $(NOECHO) $(CHMOD) 755 $(INST_ARCHLIB)
+ $(NOECHO) $(TOUCH) $(INST_ARCHLIB)$(DFSEP).exists
+
+$(INST_AUTODIR)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_AUTODIR)
+ $(NOECHO) $(CHMOD) 755 $(INST_AUTODIR)
+ $(NOECHO) $(TOUCH) $(INST_AUTODIR)$(DFSEP).exists
+
+$(INST_ARCHAUTODIR)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_ARCHAUTODIR)
+ $(NOECHO) $(CHMOD) 755 $(INST_ARCHAUTODIR)
+ $(NOECHO) $(TOUCH) $(INST_ARCHAUTODIR)$(DFSEP).exists
+
+$(INST_BIN)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_BIN)
+ $(NOECHO) $(CHMOD) 755 $(INST_BIN)
+ $(NOECHO) $(TOUCH) $(INST_BIN)$(DFSEP).exists
+
+$(INST_SCRIPT)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_SCRIPT)
+ $(NOECHO) $(CHMOD) 755 $(INST_SCRIPT)
+ $(NOECHO) $(TOUCH) $(INST_SCRIPT)$(DFSEP).exists
+
+$(INST_MAN1DIR)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_MAN1DIR)
+ $(NOECHO) $(CHMOD) 755 $(INST_MAN1DIR)
+ $(NOECHO) $(TOUCH) $(INST_MAN1DIR)$(DFSEP).exists
+
+$(INST_MAN3DIR)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_MAN3DIR)
+ $(NOECHO) $(CHMOD) 755 $(INST_MAN3DIR)
+ $(NOECHO) $(TOUCH) $(INST_MAN3DIR)$(DFSEP).exists
+
+
+
+# --- MakeMaker linkext section:
+
+linkext :: $(LINKTYPE)
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker dlsyms section:
+
+
+# --- MakeMaker dynamic section:
+
+dynamic :: $(FIRST_MAKEFILE) $(INST_DYNAMIC) $(INST_BOOT)
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker dynamic_bs section:
+
+BOOTSTRAP =
+
+
+# --- MakeMaker dynamic_lib section:
+
+
+# --- MakeMaker static section:
+
+## $(INST_PM) has been moved to the all: target.
+## It remains here for awhile to allow for old usage: "make static"
+static :: $(FIRST_MAKEFILE) $(INST_STATIC)
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker static_lib section:
+
+
+# --- MakeMaker manifypods section:
+
+POD2MAN_EXE = $(PERLRUN) "-MExtUtils::Command::MM" -e pod2man "--"
+POD2MAN = $(POD2MAN_EXE)
+
+
+manifypods : pure_all \
+ bin/process_wormbase.pl \
+ bin/make_das_conf.pl \
+ bin/load_genbank.pl \
+ bin/process_sgd.pl \
+ bin/process_gadfly.pl \
+ lib/Bio/Graphics/Glyph/trace.pm \
+ lib/Bio/Graphics/Browser/Plugin.pm \
+ lib/Bio/Graphics/Glyph/genscan_transcript.pm \
+ lib/Bio/Graphics/Browser/Realign.pm \
+ lib/Bio/Graphics/Glyph/wormbase_transcript.pm \
+ lib/Bio/Graphics/FeatureFile.pm \
+ lib/Bio/DB/GFF/Aggregator/reftranscript.pm \
+ lib/Bio/DB/Das/BioSQL/PartialSeqAdaptor.pm \
+ lib/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm \
+ lib/Bio/DB/Das/Chado/Segment/Feature.pm \
+ lib/Bio/Graphics/Glyph/ld_plot.pm \
+ lib/Bio/DB/GFF/Aggregator/waba_alignment.pm \
+ lib/Bio/DB/GFF/Aggregator/orf.pm \
+ lib/Bio/Graphics/Glyph/spectrogram.pm \
+ lib/Bio/Graphics/Browser/PadAlignment.pm \
+ lib/Bio/DB/Das/BioSQL/DBAdaptor.pm \
+ lib/Bio/Graphics/Browser.pm \
+ lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm \
+ lib/Bio/Graphics/Glyph/ideogram.pm \
+ lib/Bio/DB/Das/BioSQL/Segment.pm \
+ lib/Bio/Graphics/Browser/PluginSet.pm \
+ lib/CGI/Session/ID/salted_md5.pm \
+ lib/Bio/DB/GFF/Aggregator/match_gap.pm \
+ lib/Bio/Graphics/Glyph/heat_map.pm \
+ lib/CGI/Toggle.pm \
+ lib/Bio/Graphics/Browser/GFFhelper.pm \
+ lib/Bio/Graphics/Browser/RemoteSet.pm \
+ lib/Bio/Graphics/Glyph/insertion_chromosome.pm \
+ lib/Bio/Graphics/Glyph/pairwise_plot.pm \
+ lib/Bio/Graphics/Glyph/allele_tower.pm \
+ lib/Bio/Graphics/Browser/Util.pm \
+ lib/Bio/DB/Das/Chado.pm \
+ lib/Bio/Graphics/Browser/Markup.pm \
+ lib/Bio/Graphics/Glyph/heat_map_ideogram.pm \
+ lib/Bio/DB/Das/BioSQL.pm \
+ lib/Bio/DB/Das/Chado/Segment.pm \
+ lib/Bio/Graphics/Browser/UploadSet.pm \
+ lib/Bio/Graphics/Glyph/trace.pm \
+ lib/Bio/Graphics/Browser/Plugin.pm \
+ lib/Bio/Graphics/Glyph/genscan_transcript.pm \
+ lib/Bio/Graphics/Browser/Realign.pm \
+ lib/Bio/Graphics/Glyph/wormbase_transcript.pm \
+ lib/Bio/Graphics/FeatureFile.pm \
+ lib/Bio/DB/GFF/Aggregator/reftranscript.pm \
+ lib/Bio/DB/Das/BioSQL/PartialSeqAdaptor.pm \
+ lib/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm \
+ lib/Bio/DB/Das/Chado/Segment/Feature.pm \
+ lib/Bio/Graphics/Glyph/ld_plot.pm \
+ lib/Bio/DB/GFF/Aggregator/waba_alignment.pm \
+ lib/Bio/DB/GFF/Aggregator/orf.pm \
+ lib/Bio/Graphics/Glyph/spectrogram.pm \
+ lib/Bio/Graphics/Browser/PadAlignment.pm \
+ lib/Bio/DB/Das/BioSQL/DBAdaptor.pm \
+ lib/Bio/Graphics/Browser.pm \
+ lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm \
+ lib/Bio/Graphics/Glyph/ideogram.pm \
+ lib/Bio/DB/Das/BioSQL/Segment.pm \
+ lib/Bio/Graphics/Browser/PluginSet.pm \
+ lib/CGI/Session/ID/salted_md5.pm \
+ lib/Bio/DB/GFF/Aggregator/match_gap.pm \
+ lib/Bio/Graphics/Glyph/heat_map.pm \
+ lib/CGI/Toggle.pm \
+ lib/Bio/Graphics/Browser/GFFhelper.pm \
+ lib/Bio/Graphics/Browser/RemoteSet.pm \
+ lib/Bio/Graphics/Glyph/insertion_chromosome.pm \
+ lib/Bio/Graphics/Glyph/pairwise_plot.pm \
+ lib/Bio/Graphics/Glyph/allele_tower.pm \
+ lib/Bio/Graphics/Browser/Util.pm \
+ lib/Bio/DB/Das/Chado.pm \
+ lib/Bio/Graphics/Browser/Markup.pm \
+ lib/Bio/Graphics/Glyph/heat_map_ideogram.pm \
+ lib/Bio/DB/Das/BioSQL.pm \
+ lib/Bio/DB/Das/Chado/Segment.pm \
+ lib/Bio/Graphics/Browser/UploadSet.pm
+ $(NOECHO) $(POD2MAN) --section=$(MAN1EXT) --perm_rw=$(PERM_RW) \
+ bin/process_wormbase.pl $(INST_MAN1DIR)/process_wormbase.pl.$(MAN1EXT) \
+ bin/make_das_conf.pl $(INST_MAN1DIR)/make_das_conf.pl.$(MAN1EXT) \
+ bin/load_genbank.pl $(INST_MAN1DIR)/load_genbank.pl.$(MAN1EXT) \
+ bin/process_sgd.pl $(INST_MAN1DIR)/process_sgd.pl.$(MAN1EXT) \
+ bin/process_gadfly.pl $(INST_MAN1DIR)/process_gadfly.pl.$(MAN1EXT)
+ $(NOECHO) $(POD2MAN) --section=$(MAN3EXT) --perm_rw=$(PERM_RW) \
+ lib/Bio/Graphics/Glyph/trace.pm $(INST_MAN3DIR)/Bio::Graphics::Glyph::trace.$(MAN3EXT) \
+ lib/Bio/Graphics/Browser/Plugin.pm $(INST_MAN3DIR)/Bio::Graphics::Browser::Plugin.$(MAN3EXT) \
+ lib/Bio/Graphics/Glyph/genscan_transcript.pm $(INST_MAN3DIR)/Bio::Graphics::Glyph::genscan_transcript.$(MAN3EXT) \
+ lib/Bio/Graphics/Browser/Realign.pm $(INST_MAN3DIR)/Bio::Graphics::Browser::Realign.$(MAN3EXT) \
+ lib/Bio/Graphics/Glyph/wormbase_transcript.pm $(INST_MAN3DIR)/Bio::Graphics::Glyph::wormbase_transcript.$(MAN3EXT) \
+ lib/Bio/Graphics/FeatureFile.pm $(INST_MAN3DIR)/Bio::Graphics::FeatureFile.$(MAN3EXT) \
+ lib/Bio/DB/GFF/Aggregator/reftranscript.pm $(INST_MAN3DIR)/Bio::DB::GFF::Aggregator::reftranscript.$(MAN3EXT) \
+ lib/Bio/DB/Das/BioSQL/PartialSeqAdaptor.pm $(INST_MAN3DIR)/Bio::DB::Das::BioSQL::PartialSeqAdaptor.$(MAN3EXT) \
+ lib/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm $(INST_MAN3DIR)/Bio::DB::Das::BioSQL::BioDatabaseAdaptor.$(MAN3EXT) \
+ lib/Bio/DB/Das/Chado/Segment/Feature.pm $(INST_MAN3DIR)/Bio::DB::Das::Chado::Segment::Feature.$(MAN3EXT) \
+ lib/Bio/Graphics/Glyph/ld_plot.pm $(INST_MAN3DIR)/Bio::Graphics::Glyph::ld_plot.$(MAN3EXT) \
+ lib/Bio/DB/GFF/Aggregator/waba_alignment.pm $(INST_MAN3DIR)/Bio::DB::GFF::Aggregator::waba_alignment.$(MAN3EXT) \
+ lib/Bio/DB/GFF/Aggregator/orf.pm $(INST_MAN3DIR)/Bio::DB::GFF::Aggregator::orf.$(MAN3EXT) \
+ lib/Bio/Graphics/Glyph/spectrogram.pm $(INST_MAN3DIR)/Bio::Graphics::Glyph::spectrogram.$(MAN3EXT) \
+ lib/Bio/Graphics/Browser/PadAlignment.pm $(INST_MAN3DIR)/Bio::Graphics::Browser::PadAlignment.$(MAN3EXT) \
+ lib/Bio/DB/Das/BioSQL/DBAdaptor.pm $(INST_MAN3DIR)/Bio::DB::Das::BioSQL::DBAdaptor.$(MAN3EXT) \
+ lib/Bio/Graphics/Browser.pm $(INST_MAN3DIR)/Bio::Graphics::Browser.$(MAN3EXT) \
+ lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm $(INST_MAN3DIR)/Bio::DB::GFF::Aggregator::wormbase_gene.$(MAN3EXT) \
+ lib/Bio/Graphics/Glyph/ideogram.pm $(INST_MAN3DIR)/Bio::Graphics::Glyph::ideogram.$(MAN3EXT) \
+ lib/Bio/DB/Das/BioSQL/Segment.pm $(INST_MAN3DIR)/Bio::DB::Das::BioSQL::Segment.$(MAN3EXT) \
+ lib/Bio/Graphics/Browser/PluginSet.pm $(INST_MAN3DIR)/Bio::Graphics::Browser::PluginSet.$(MAN3EXT) \
+ lib/CGI/Session/ID/salted_md5.pm $(INST_MAN3DIR)/CGI::Session::ID::salted_md5.$(MAN3EXT) \
+ lib/Bio/DB/GFF/Aggregator/match_gap.pm $(INST_MAN3DIR)/Bio::DB::GFF::Aggregator::match_gap.$(MAN3EXT) \
+ lib/Bio/Graphics/Glyph/heat_map.pm $(INST_MAN3DIR)/Bio::Graphics::Glyph::heat_map.$(MAN3EXT) \
+ lib/CGI/Toggle.pm $(INST_MAN3DIR)/CGI::Toggle.$(MAN3EXT) \
+ lib/Bio/Graphics/Browser/GFFhelper.pm $(INST_MAN3DIR)/Bio::Graphics::Browser::GFFhelper.$(MAN3EXT) \
+ lib/Bio/Graphics/Browser/RemoteSet.pm $(INST_MAN3DIR)/Bio::Graphics::Browser::RemoteSet.$(MAN3EXT) \
+ lib/Bio/Graphics/Glyph/insertion_chromosome.pm $(INST_MAN3DIR)/Bio::Graphics::Glyph::insertion_chromosome.$(MAN3EXT) \
+ lib/Bio/Graphics/Glyph/pairwise_plot.pm $(INST_MAN3DIR)/Bio::Graphics::Glyph::pairwise_plot.$(MAN3EXT) \
+ lib/Bio/Graphics/Glyph/allele_tower.pm $(INST_MAN3DIR)/Bio::Graphics::Glyph::allele_tower.$(MAN3EXT) \
+ lib/Bio/Graphics/Browser/Util.pm $(INST_MAN3DIR)/Bio::Graphics::Browser::Util.$(MAN3EXT) \
+ lib/Bio/DB/Das/Chado.pm $(INST_MAN3DIR)/Bio::DB::Das::Chado.$(MAN3EXT) \
+ lib/Bio/Graphics/Browser/Markup.pm $(INST_MAN3DIR)/Bio::Graphics::Browser::Markup.$(MAN3EXT) \
+ lib/Bio/Graphics/Glyph/heat_map_ideogram.pm $(INST_MAN3DIR)/Bio::Graphics::Glyph::heat_map_ideogram.$(MAN3EXT) \
+ lib/Bio/DB/Das/BioSQL.pm $(INST_MAN3DIR)/Bio::DB::Das::BioSQL.$(MAN3EXT) \
+ lib/Bio/DB/Das/Chado/Segment.pm $(INST_MAN3DIR)/Bio::DB::Das::Chado::Segment.$(MAN3EXT) \
+ lib/Bio/Graphics/Browser/UploadSet.pm $(INST_MAN3DIR)/Bio::Graphics::Browser::UploadSet.$(MAN3EXT)
+
+
+
+
+# --- MakeMaker processPL section:
+
+all :: bin/load_genbank.pl
+ $(NOECHO) $(NOOP)
+
+bin/load_genbank.pl :: bin/load_genbank.PLS pm_to_blib
+ $(PERLRUNINST) bin/load_genbank.PLS bin/load_genbank.pl
+
+all :: bin/make_das_conf.pl
+ $(NOECHO) $(NOOP)
+
+bin/make_das_conf.pl :: bin/make_das_conf.PLS pm_to_blib
+ $(PERLRUNINST) bin/make_das_conf.PLS bin/make_das_conf.pl
+
+all :: bin/process_gadfly.pl
+ $(NOECHO) $(NOOP)
+
+bin/process_gadfly.pl :: bin/process_gadfly.PLS pm_to_blib
+ $(PERLRUNINST) bin/process_gadfly.PLS bin/process_gadfly.pl
+
+all :: bin/process_sgd.pl
+ $(NOECHO) $(NOOP)
+
+bin/process_sgd.pl :: bin/process_sgd.PLS pm_to_blib
+ $(PERLRUNINST) bin/process_sgd.PLS bin/process_sgd.pl
+
+all :: bin/process_wormbase.pl
+ $(NOECHO) $(NOOP)
+
+bin/process_wormbase.pl :: bin/process_wormbase.PLS pm_to_blib
+ $(PERLRUNINST) bin/process_wormbase.PLS bin/process_wormbase.pl
+
+all :: bin/register_moby_services.pl
+ $(NOECHO) $(NOOP)
+
+bin/register_moby_services.pl :: bin/register_moby_services.PLS pm_to_blib
+ $(PERLRUNINST) bin/register_moby_services.PLS bin/register_moby_services.pl
+
+all :: bin/ucsc_genes2gff.pl
+ $(NOECHO) $(NOOP)
+
+bin/ucsc_genes2gff.pl :: bin/ucsc_genes2gff.PLS pm_to_blib
+ $(PERLRUNINST) bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
+
+all :: cgi-bin/das
+ $(NOECHO) $(NOOP)
+
+cgi-bin/das :: cgi-bin/das.PLS pm_to_blib
+ $(PERLRUNINST) cgi-bin/das.PLS cgi-bin/das
+
+all :: cgi-bin/gbrowse
+ $(NOECHO) $(NOOP)
+
+cgi-bin/gbrowse : FORCE
+ $(PERLRUNINST) cgi-bin/gbrowse.PLS cgi-bin/gbrowse
+
+all :: cgi-bin/gbrowse_details
+ $(NOECHO) $(NOOP)
+
+cgi-bin/gbrowse_details : FORCE
+ $(PERLRUNINST) cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
+
+all :: cgi-bin/gbrowse_est
+ $(NOECHO) $(NOOP)
+
+cgi-bin/gbrowse_est : FORCE
+ $(PERLRUNINST) cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
+
+all :: cgi-bin/gbrowse_img
+ $(NOECHO) $(NOOP)
+
+cgi-bin/gbrowse_img : FORCE
+ $(PERLRUNINST) cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
+
+all :: cgi-bin/gbrowse_moby
+ $(NOECHO) $(NOOP)
+
+cgi-bin/gbrowse_moby : FORCE
+ $(PERLRUNINST) cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
+
+all :: cgi-bin/moby_server
+ $(NOECHO) $(NOOP)
+
+cgi-bin/moby_server :: cgi-bin/moby_server.PLS pm_to_blib
+ $(PERLRUNINST) cgi-bin/moby_server.PLS cgi-bin/moby_server
+
+all :: conf/MobyServices/GbrowseServices.pm
+ $(NOECHO) $(NOOP)
+
+conf/MobyServices/GbrowseServices.pm :: conf/MobyServices/GbrowseServices.PMS pm_to_blib
+ $(PERLRUNINST) conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
+
+all :: install_util/cgi_install.pl
+ $(NOECHO) $(NOOP)
+
+install_util/cgi_install.pl :: install_util/cgi_install.PLS pm_to_blib
+ $(PERLRUNINST) install_util/cgi_install.PLS install_util/cgi_install.pl
+
+all :: install_util/conf_install.pl
+ $(NOECHO) $(NOOP)
+
+install_util/conf_install.pl :: install_util/conf_install.PLS pm_to_blib
+ $(PERLRUNINST) install_util/conf_install.PLS install_util/conf_install.pl
+
+all :: install_util/gbrowse_ppm_install.pl
+ $(NOECHO) $(NOOP)
+
+install_util/gbrowse_ppm_install.pl :: install_util/gbrowse_ppm_install.PLS pm_to_blib
+ $(PERLRUNINST) install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
+
+all :: install_util/htdocs_install.pl
+ $(NOECHO) $(NOOP)
+
+install_util/htdocs_install.pl :: install_util/htdocs_install.PLS pm_to_blib
+ $(PERLRUNINST) install_util/htdocs_install.PLS install_util/htdocs_install.pl
+
+
+# --- MakeMaker installbin section:
+
+EXE_FILES = bin/register_moby_services.pl bin/make_das_conf.pl bin/process_wormbase.pl bin/process_sgd.pl bin/process_gadfly.pl bin/load_genbank.pl
+
+pure_all :: $(INST_SCRIPT)/process_wormbase.pl $(INST_SCRIPT)/make_das_conf.pl $(INST_SCRIPT)/load_genbank.pl $(INST_SCRIPT)/process_sgd.pl $(INST_SCRIPT)/register_moby_services.pl $(INST_SCRIPT)/process_gadfly.pl
+ $(NOECHO) $(NOOP)
+
+realclean ::
+ $(RM_F) \
+ $(INST_SCRIPT)/process_wormbase.pl $(INST_SCRIPT)/make_das_conf.pl \
+ $(INST_SCRIPT)/load_genbank.pl $(INST_SCRIPT)/process_sgd.pl \
+ $(INST_SCRIPT)/register_moby_services.pl $(INST_SCRIPT)/process_gadfly.pl
+
+$(INST_SCRIPT)/process_wormbase.pl : bin/process_wormbase.pl $(FIRST_MAKEFILE) $(INST_SCRIPT)$(DFSEP).exists $(INST_BIN)$(DFSEP).exists
+ $(NOECHO) $(RM_F) $(INST_SCRIPT)/process_wormbase.pl
+ $(CP) bin/process_wormbase.pl $(INST_SCRIPT)/process_wormbase.pl
+ $(FIXIN) $(INST_SCRIPT)/process_wormbase.pl
+ -$(NOECHO) $(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/process_wormbase.pl
+
+$(INST_SCRIPT)/make_das_conf.pl : bin/make_das_conf.pl $(FIRST_MAKEFILE) $(INST_SCRIPT)$(DFSEP).exists $(INST_BIN)$(DFSEP).exists
+ $(NOECHO) $(RM_F) $(INST_SCRIPT)/make_das_conf.pl
+ $(CP) bin/make_das_conf.pl $(INST_SCRIPT)/make_das_conf.pl
+ $(FIXIN) $(INST_SCRIPT)/make_das_conf.pl
+ -$(NOECHO) $(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/make_das_conf.pl
+
+$(INST_SCRIPT)/load_genbank.pl : bin/load_genbank.pl $(FIRST_MAKEFILE) $(INST_SCRIPT)$(DFSEP).exists $(INST_BIN)$(DFSEP).exists
+ $(NOECHO) $(RM_F) $(INST_SCRIPT)/load_genbank.pl
+ $(CP) bin/load_genbank.pl $(INST_SCRIPT)/load_genbank.pl
+ $(FIXIN) $(INST_SCRIPT)/load_genbank.pl
+ -$(NOECHO) $(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/load_genbank.pl
+
+$(INST_SCRIPT)/process_sgd.pl : bin/process_sgd.pl $(FIRST_MAKEFILE) $(INST_SCRIPT)$(DFSEP).exists $(INST_BIN)$(DFSEP).exists
+ $(NOECHO) $(RM_F) $(INST_SCRIPT)/process_sgd.pl
+ $(CP) bin/process_sgd.pl $(INST_SCRIPT)/process_sgd.pl
+ $(FIXIN) $(INST_SCRIPT)/process_sgd.pl
+ -$(NOECHO) $(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/process_sgd.pl
+
+$(INST_SCRIPT)/register_moby_services.pl : bin/register_moby_services.pl $(FIRST_MAKEFILE) $(INST_SCRIPT)$(DFSEP).exists $(INST_BIN)$(DFSEP).exists
+ $(NOECHO) $(RM_F) $(INST_SCRIPT)/register_moby_services.pl
+ $(CP) bin/register_moby_services.pl $(INST_SCRIPT)/register_moby_services.pl
+ $(FIXIN) $(INST_SCRIPT)/register_moby_services.pl
+ -$(NOECHO) $(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/register_moby_services.pl
+
+$(INST_SCRIPT)/process_gadfly.pl : bin/process_gadfly.pl $(FIRST_MAKEFILE) $(INST_SCRIPT)$(DFSEP).exists $(INST_BIN)$(DFSEP).exists
+ $(NOECHO) $(RM_F) $(INST_SCRIPT)/process_gadfly.pl
+ $(CP) bin/process_gadfly.pl $(INST_SCRIPT)/process_gadfly.pl
+ $(FIXIN) $(INST_SCRIPT)/process_gadfly.pl
+ -$(NOECHO) $(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/process_gadfly.pl
+
+
+
+# --- MakeMaker subdirs section:
+
+# The default clean, realclean and test targets in this Makefile
+# have automatically been given entries for each subdir.
+
+
+subdirs ::
+ $(NOECHO) cd libalign && $(MAKE) $(USEMAKEFILE) $(FIRST_MAKEFILE) all $(PASTHRU)
+
+
+# --- MakeMaker clean_subdirs section:
+clean_subdirs :
+ $(ABSPERLRUN) -e 'chdir '\''libalign'\''; system '\''$(MAKE) clean'\'' if -f '\''$(FIRST_MAKEFILE)'\'';'
+
+
+# --- MakeMaker clean section:
+
+# Delete temporary files but do not touch installed files. We don't delete
+# the Makefile here so a later make realclean still has a makefile to use.
+
+clean :: clean_subdirs
+ - $(RM_F) \
+ *$(LIB_EXT) core \
+ core.[0-9] $(INST_ARCHAUTODIR)/extralibs.all \
+ core.[0-9][0-9] $(BASEEXT).bso \
+ pm_to_blib.ts core.[0-9][0-9][0-9][0-9] \
+ $(BASEEXT).x $(BOOTSTRAP) \
+ perl$(EXE_EXT) tmon.out \
+ *$(OBJ_EXT) pm_to_blib \
+ $(INST_ARCHAUTODIR)/extralibs.ld blibdirs.ts \
+ core.[0-9][0-9][0-9][0-9][0-9] *perl.core \
+ core.*perl.*.? $(MAKE_APERL_FILE) \
+ $(BASEEXT).def perl \
+ core.[0-9][0-9][0-9] mon.out \
+ lib$(BASEEXT).def perl.exe \
+ perlmain.c so_locations \
+ $(BASEEXT).exp
+ - $(RM_RF) \
+ blib
+ - $(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD) $(DEV_NULL)
+ -$(PERL) install_util/make_clean_add.pl
+
+
+# --- MakeMaker realclean_subdirs section:
+realclean_subdirs :
+ - $(ABSPERLRUN) -e 'chdir '\''libalign'\''; system '\''$(MAKE) $(USEMAKEFILE) $(MAKEFILE_OLD) realclean'\'' if -f '\''$(MAKEFILE_OLD)'\'';'
+ - $(ABSPERLRUN) -e 'chdir '\''libalign'\''; system '\''$(MAKE) $(USEMAKEFILE) $(FIRST_MAKEFILE) realclean'\'' if -f '\''$(FIRST_MAKEFILE)'\'';'
+
+
+# --- MakeMaker realclean section:
+# Delete temporary files (via clean) and also delete dist files
+realclean purge :: clean realclean_subdirs
+ - $(RM_F) \
+ $(MAKEFILE_OLD) $(FIRST_MAKEFILE)
+ - $(RM_RF) \
+ $(DISTVNAME)
+
+
+# --- MakeMaker metafile section:
+metafile : create_distdir
+ $(NOECHO) $(ECHO) Generating META.yml
+ $(NOECHO) $(ECHO) '# http://module-build.sourceforge.net/META-spec.html' > META_new.yml
+ $(NOECHO) $(ECHO) '#XXXXXXX This is a prototype!!! It will change in the future!!! XXXXX#' >> META_new.yml
+ $(NOECHO) $(ECHO) 'name: Generic-Genome-Browser' >> META_new.yml
+ $(NOECHO) $(ECHO) 'version: 1.68' >> META_new.yml
+ $(NOECHO) $(ECHO) 'version_from: ' >> META_new.yml
+ $(NOECHO) $(ECHO) 'installdirs: vendor' >> META_new.yml
+ $(NOECHO) $(ECHO) 'requires:' >> META_new.yml
+ $(NOECHO) $(ECHO) ' Bio::Perl: 1.005002' >> META_new.yml
+ $(NOECHO) $(ECHO) ' CGI::Session: 4.02' >> META_new.yml
+ $(NOECHO) $(ECHO) ' Class::Base: 0' >> META_new.yml
+ $(NOECHO) $(ECHO) ' Digest::MD5: 0' >> META_new.yml
+ $(NOECHO) $(ECHO) ' File::Temp: 0' >> META_new.yml
+ $(NOECHO) $(ECHO) ' GD: 2.07' >> META_new.yml
+ $(NOECHO) $(ECHO) ' IO::String: 0' >> META_new.yml
+ $(NOECHO) $(ECHO) ' Text::Shellwords: 1.08' >> META_new.yml
+ $(NOECHO) $(ECHO) '' >> META_new.yml
+ $(NOECHO) $(ECHO) 'distribution_type: module' >> META_new.yml
+ $(NOECHO) $(ECHO) 'generated_by: ExtUtils::MakeMaker version 6.30_01' >> META_new.yml
+ -$(NOECHO) $(MV) META_new.yml $(DISTVNAME)/META.yml
+
+
+# --- MakeMaker signature section:
+signature :
+ cpansign -s
+
+
+# --- MakeMaker dist_basics section:
+distclean :: realclean distcheck
+ $(NOECHO) $(NOOP)
+
+distcheck :
+ $(PERLRUN) "-MExtUtils::Manifest=fullcheck" -e fullcheck
+
+skipcheck :
+ $(PERLRUN) "-MExtUtils::Manifest=skipcheck" -e skipcheck
+
+manifest :
+ $(PERLRUN) "-MExtUtils::Manifest=mkmanifest" -e mkmanifest
+
+veryclean : realclean
+ $(RM_F) *~ *.orig */*~ */*.orig
+
+
+
+# --- MakeMaker dist_core section:
+
+dist : $(DIST_DEFAULT) $(FIRST_MAKEFILE)
+ $(NOECHO) $(ABSPERLRUN) -l -e 'print '\''Warning: Makefile possibly out of date with $(VERSION_FROM)'\''' \
+ -e ' if -e '\''$(VERSION_FROM)'\'' and -M '\''$(VERSION_FROM)'\'' < -M '\''$(FIRST_MAKEFILE)'\'';'
+
+tardist : $(DISTVNAME).tar$(SUFFIX)
+ $(NOECHO) $(NOOP)
+
+uutardist : $(DISTVNAME).tar$(SUFFIX)
+ uuencode $(DISTVNAME).tar$(SUFFIX) $(DISTVNAME).tar$(SUFFIX) > $(DISTVNAME).tar$(SUFFIX)_uu
+
+$(DISTVNAME).tar$(SUFFIX) : distdir
+ $(PREOP)
+ $(TO_UNIX)
+ $(TAR) $(TARFLAGS) $(DISTVNAME).tar $(DISTVNAME)
+ $(RM_RF) $(DISTVNAME)
+ $(COMPRESS) $(DISTVNAME).tar
+ $(POSTOP)
+
+zipdist : $(DISTVNAME).zip
+ $(NOECHO) $(NOOP)
+
+$(DISTVNAME).zip : distdir
+ $(PREOP)
+ $(ZIP) $(ZIPFLAGS) $(DISTVNAME).zip $(DISTVNAME)
+ $(RM_RF) $(DISTVNAME)
+ $(POSTOP)
+
+shdist : distdir
+ $(PREOP)
+ $(SHAR) $(DISTVNAME) > $(DISTVNAME).shar
+ $(RM_RF) $(DISTVNAME)
+ $(POSTOP)
+
+
+# --- MakeMaker distdir section:
+create_distdir :
+ $(RM_RF) $(DISTVNAME)
+ $(PERLRUN) "-MExtUtils::Manifest=manicopy,maniread" \
+ -e "manicopy(maniread(),'$(DISTVNAME)', '$(DIST_CP)');"
+
+distdir : create_distdir distmeta
+ $(NOECHO) $(NOOP)
+
+
+
+# --- MakeMaker dist_test section:
+disttest : distdir
+ cd $(DISTVNAME) && $(ABSPERLRUN) Makefile.PL "DESTDIR=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse" "INSTALLDIRS=vendor" "VENDORARCHEXP=/usr/share/perl5"
+ cd $(DISTVNAME) && $(MAKE) $(PASTHRU)
+ cd $(DISTVNAME) && $(MAKE) test $(PASTHRU)
+
+
+
+# --- MakeMaker dist_ci section:
+
+ci :
+ $(PERLRUN) "-MExtUtils::Manifest=maniread" \
+ -e "@all = keys %{ maniread() };" \
+ -e "print(qq{Executing $(CI) @all\n}); system(qq{$(CI) @all});" \
+ -e "print(qq{Executing $(RCS_LABEL) ...\n}); system(qq{$(RCS_LABEL) @all});"
+
+
+# --- MakeMaker distmeta section:
+distmeta : create_distdir metafile
+ $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{META.yml} => q{Module meta-data (added by MakeMaker)}}) } ' \
+ -e ' or print "Could not add META.yml to MANIFEST: $${'\''@'\''}\n"'
+
+
+
+# --- MakeMaker distsignature section:
+distsignature : create_distdir
+ $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{SIGNATURE} => q{Public-key signature (added by MakeMaker)}}) } ' \
+ -e ' or print "Could not add SIGNATURE to MANIFEST: $${'\''@'\''}\n"'
+ $(NOECHO) cd $(DISTVNAME) && $(TOUCH) SIGNATURE
+ cd $(DISTVNAME) && cpansign -s
+
+
+
+# --- MakeMaker install section:
+
+install :: all pure_install doc_install conf_install cgi_install htdocs_install
+ $(NOECHO) $(NOOP)
+
+install_perl :: all pure_perl_install doc_perl_install
+ $(NOECHO) $(NOOP)
+
+install_site :: all pure_site_install doc_site_install
+ $(NOECHO) $(NOOP)
+
+install_vendor :: all pure_vendor_install doc_vendor_install
+ $(NOECHO) $(NOOP)
+
+pure_install :: pure_$(INSTALLDIRS)_install
+ $(NOECHO) $(NOOP)
+
+doc_install :: doc_$(INSTALLDIRS)_install
+ $(NOECHO) $(NOOP)
+
+pure__install : pure_site_install
+ $(NOECHO) $(ECHO) INSTALLDIRS not defined, defaulting to INSTALLDIRS=site
+
+doc__install : doc_site_install
+ $(NOECHO) $(ECHO) INSTALLDIRS not defined, defaulting to INSTALLDIRS=site
+
+pure_perl_install ::
+ $(NOECHO) umask 022; $(MOD_INSTALL) \
+ $(INST_LIB) $(DESTINSTALLPRIVLIB) \
+ $(INST_ARCHLIB) $(DESTINSTALLARCHLIB) \
+ $(INST_BIN) $(DESTINSTALLBIN) \
+ $(INST_SCRIPT) $(DESTINSTALLSCRIPT) \
+ $(INST_MAN1DIR) $(DESTINSTALLMAN1DIR) \
+ $(INST_MAN3DIR) $(DESTINSTALLMAN3DIR)
+ $(NOECHO) $(WARN_IF_OLD_PACKLIST) \
+ $(SITEARCHEXP)/auto/$(FULLEXT)
+
+
+pure_site_install ::
+ $(NOECHO) umask 02; $(MOD_INSTALL) \
+ read $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist \
+ write $(DESTINSTALLSITEARCH)/auto/$(FULLEXT)/.packlist \
+ $(INST_LIB) $(DESTINSTALLSITELIB) \
+ $(INST_ARCHLIB) $(DESTINSTALLSITEARCH) \
+ $(INST_BIN) $(DESTINSTALLSITEBIN) \
+ $(INST_SCRIPT) $(DESTINSTALLSITESCRIPT) \
+ $(INST_MAN1DIR) $(DESTINSTALLSITEMAN1DIR) \
+ $(INST_MAN3DIR) $(DESTINSTALLSITEMAN3DIR)
+ $(NOECHO) $(WARN_IF_OLD_PACKLIST) \
+ $(PERL_ARCHLIB)/auto/$(FULLEXT)
+
+pure_vendor_install ::
+ $(NOECHO) umask 022; $(MOD_INSTALL) \
+ $(INST_LIB) $(DESTINSTALLVENDORLIB) \
+ $(INST_ARCHLIB) $(DESTINSTALLVENDORARCH) \
+ $(INST_BIN) $(DESTINSTALLVENDORBIN) \
+ $(INST_SCRIPT) $(DESTINSTALLVENDORSCRIPT) \
+ $(INST_MAN1DIR) $(DESTINSTALLVENDORMAN1DIR) \
+ $(INST_MAN3DIR) $(DESTINSTALLVENDORMAN3DIR)
+
+doc_perl_install ::
+
+doc_site_install ::
+ $(NOECHO) $(ECHO) Appending installation info to $(DESTINSTALLSITEARCH)/perllocal.pod
+ -$(NOECHO) umask 02; $(MKPATH) $(DESTINSTALLSITEARCH)
+ -$(NOECHO) umask 02; $(DOC_INSTALL) \
+ "Module" "$(NAME)" \
+ "installed into" "$(INSTALLSITELIB)" \
+ LINKTYPE "$(LINKTYPE)" \
+ VERSION "$(VERSION)" \
+ EXE_FILES "$(EXE_FILES)" \
+ >> $(DESTINSTALLSITEARCH)/perllocal.pod
+
+doc_vendor_install ::
+
+
+uninstall :: uninstall_from_$(INSTALLDIRS)dirs
+ $(NOECHO) $(NOOP)
+
+uninstall_from_perldirs ::
+
+uninstall_from_sitedirs ::
+ $(NOECHO) $(UNINSTALL) $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist
+
+uninstall_from_vendordirs ::
+
+
+
+# --- MakeMaker force section:
+# Phony target to force checking subdirectories.
+FORCE:
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker perldepend section:
+
+
+# --- MakeMaker makefile section:
+# We take a very conservative approach here, but it's worth it.
+# We move Makefile to Makefile.old here to avoid gnu make looping.
+$(FIRST_MAKEFILE) : Makefile.PL $(CONFIGDEP)
+ $(NOECHO) $(ECHO) "Makefile out-of-date with respect to $?"
+ $(NOECHO) $(ECHO) "Cleaning current config before rebuilding Makefile..."
+ -$(NOECHO) $(RM_F) $(MAKEFILE_OLD)
+ -$(NOECHO) $(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD)
+ - $(MAKE) $(USEMAKEFILE) $(MAKEFILE_OLD) clean $(DEV_NULL)
+ $(PERLRUN) Makefile.PL "DESTDIR=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse" "INSTALLDIRS=vendor" "VENDORARCHEXP=/usr/share/perl5"
+ $(NOECHO) $(ECHO) "==> Your Makefile has been rebuilt. <=="
+ $(NOECHO) $(ECHO) "==> Please rerun the $(MAKE) command. <=="
+ false
+
+
+
+# --- MakeMaker staticmake section:
+
+# --- MakeMaker makeaperl section ---
+MAP_TARGET = perl
+FULLPERL = /usr/bin/perl
+
+$(MAP_TARGET) :: static $(MAKE_APERL_FILE)
+ $(MAKE) $(USEMAKEFILE) $(MAKE_APERL_FILE) $@
+
+$(MAKE_APERL_FILE) : $(FIRST_MAKEFILE) pm_to_blib
+ $(NOECHO) $(ECHO) Writing \"$(MAKE_APERL_FILE)\" for this $(MAP_TARGET)
+ $(NOECHO) $(PERLRUNINST) \
+ Makefile.PL DIR=libalign \
+ MAKEFILE=$(MAKE_APERL_FILE) LINKTYPE=static \
+ MAKEAPERL=1 NORECURS=1 CCCDLFLAGS= \
+ DESTDIR=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse \
+ INSTALLDIRS=vendor \
+ VENDORARCHEXP=/usr/share/perl5
+
+
+# --- MakeMaker test section:
+
+TEST_VERBOSE=0
+TEST_TYPE=test_$(LINKTYPE)
+TEST_FILE = test.pl
+TEST_FILES = t/*.t
+TESTDB_SW = -d
+
+testdb :: testdb_$(LINKTYPE)
+
+test :: $(TEST_TYPE)
+ $(NOECHO) $(ABSPERLRUN) -e 'chdir '\''libalign'\''; ' \
+ -e 'system '\''$(MAKE) test $(PASTHRU)'\'' ' \
+ -e ' if -f '\''$(FIRST_MAKEFILE)'\'';'
+
+test_dynamic :: pure_all
+ PERL_DL_NONLAZY=1 $(FULLPERLRUN) "-MExtUtils::Command::MM" "-e" "test_harness($(TEST_VERBOSE), '$(INST_LIB)', '$(INST_ARCHLIB)')" $(TEST_FILES)
+
+testdb_dynamic :: pure_all
+ PERL_DL_NONLAZY=1 $(FULLPERLRUN) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
+
+test_ : test_dynamic
+
+test_static :: pure_all $(MAP_TARGET)
+ PERL_DL_NONLAZY=1 ./$(MAP_TARGET) "-MExtUtils::Command::MM" "-e" "test_harness($(TEST_VERBOSE), '$(INST_LIB)', '$(INST_ARCHLIB)')" $(TEST_FILES)
+
+testdb_static :: pure_all $(MAP_TARGET)
+ PERL_DL_NONLAZY=1 ./$(MAP_TARGET) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
+
+
+
+# --- MakeMaker ppd section:
+# Creates a PPD (Perl Package Description) for a binary distribution.
+ppd:
+ $(NOECHO) $(ECHO) '<SOFTPKG NAME="$(DISTNAME)" VERSION="1,68,0,0">' > $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <TITLE>$(DISTNAME)</TITLE>' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <ABSTRACT>A CGI-driven browser for genomic annotations.</ABSTRACT>' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <AUTHOR>Lincoln Stein (lstein at cshl.org)</AUTHOR>' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <IMPLEMENTATION>' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="Bio-Perl" VERSION="1,005002,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="CGI-Session" VERSION="4,02,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="Class-Base" VERSION="0,0,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="Digest-MD5" VERSION="0,0,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="File-Temp" VERSION="0,0,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="GD" VERSION="2,07,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="IO-String" VERSION="0,0,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="Text-Shellwords" VERSION="1,08,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <OS NAME="MSWin32" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <ARCHITECTURE NAME="MSWin32-x86-multi-thread" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <CODEBASE HREF="" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' </IMPLEMENTATION>' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <IMPLEMENTATION>' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="Bio-Perl" VERSION="1,005002,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="CGI-Session" VERSION="4,02,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="Class-Base" VERSION="0,0,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="Digest-MD5" VERSION="0,0,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="File-Temp" VERSION="0,0,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="GD" VERSION="2,07,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="IO-String" VERSION="0,0,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <DEPENDENCY NAME="Text-Shellwords" VERSION="1,08,0,0" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <OS NAME="MSWin32" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <ARCHITECTURE NAME="MSWin32-x86-multi-thread-5.8" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <CODEBASE HREF="" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' </IMPLEMENTATION>' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) '</SOFTPKG>' >> $(DISTNAME).ppd
+
+ @echo "creating Generic-Genome-Browser.ppd"
+ @echo "creating gbrowse_ppm_support_files-1.68.tar.gz"
+ @$(TAR) zcf gbrowse_ppm_support_files-1.68.tar.gz --exclude CVS --exclude '*~' --exclude '*.PLS' --exclude '.*' --exclude README --exclude '#*' DISCLAIMER INSTALL docs htdocs conf cgi-bin install_util sample_data contrib
+ @echo "creating gbrowse_ppm-1.68.tar.gz"
+ @$(TAR) zcf gbrowse_ppm-1.68.tar.gz --exclude man1 --exclude man3 blib
+ @perl -pi -e 's!HREF=""!HREF="http://www.gmod.org/ggb/ppm/gbrowse_ppm-1.68.tar.gz"!' Generic-Genome-Browser.ppd
+ @perl -pi -e 's!(\s*</IMPLEMENTATION>)!\t\t<INSTALL HREF="http://www.gmod.org/ggb/ppm/gbrowse_ppm_install.pl" EXEC="PPM_PERL" />\n\1!' Generic-Genome-Browser.ppd
+ @perl -pi -e 's!Bio-Perl!bioperl!' Generic-Genome-Browser.ppd
+ @cp install_util/gbrowse_ppm_install.pl .
+
+
+# --- MakeMaker pm_to_blib section:
+
+pm_to_blib : $(TO_INST_PM)
+ $(NOECHO) $(ABSPERLRUN) -MExtUtils::Install -e 'pm_to_blib({@ARGV}, '\''$(INST_LIB)/auto'\'', '\''$(PM_FILTER)'\'')' \
+ lib/Bio/Graphics/Glyph/trace.pm blib/lib/Bio/Graphics/Glyph/trace.pm \
+ lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm \
+ lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm \
+ lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm \
+ lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm \
+ lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm \
+ lib/Bio/Graphics/FeatureFile.pm blib/lib/Bio/Graphics/FeatureFile.pm \
+ lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm \
+ lib/Bio/DB/Das/BioSQL/PartialSeqAdaptor.pm blib/lib/Bio/DB/Das/BioSQL/PartialSeqAdaptor.pm \
+ lib/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm blib/lib/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm \
+ lib/Bio/DB/Das/Chado/Segment/Feature.pm blib/lib/Bio/DB/Das/Chado/Segment/Feature.pm \
+ lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm \
+ lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm \
+ lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm \
+ lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm \
+ lib/Bio/Graphics/Glyph/spectrogram.pm blib/lib/Bio/Graphics/Glyph/spectrogram.pm \
+ lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm \
+ lib/Bio/DB/Das/BioSQL/Iterator.pm blib/lib/Bio/DB/Das/BioSQL/Iterator.pm \
+ lib/Bio/DB/Das/BioSQL/DBAdaptor.pm blib/lib/Bio/DB/Das/BioSQL/DBAdaptor.pm \
+ lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm \
+ lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm \
+ lib/Bio/Graphics/Glyph/ideogram.pm blib/lib/Bio/Graphics/Glyph/ideogram.pm \
+ lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm \
+ lib/Bio/DB/Das/BioSQL/Segment.pm blib/lib/Bio/DB/Das/BioSQL/Segment.pm \
+ lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm \
+ lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm \
+ lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm \
+ lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm \
+ lib/Bio/Graphics/Glyph/heat_map.pm blib/lib/Bio/Graphics/Glyph/heat_map.pm \
+ lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm \
+ lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm \
+ lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm \
+ lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm \
+ lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm \
+ lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm \
+ lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm \
+ lib/Bio/DB/Das/Chado.pm blib/lib/Bio/DB/Das/Chado.pm \
+ lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm \
+ lib/Bio/Graphics/Glyph/heat_map_ideogram.pm blib/lib/Bio/Graphics/Glyph/heat_map_ideogram.pm \
+ lib/Bio/DB/Das/BioSQL.pm blib/lib/Bio/DB/Das/BioSQL.pm \
+ lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm \
+ lib/Bio/DB/Das/Chado/Segment.pm blib/lib/Bio/DB/Das/Chado/Segment.pm \
+ lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
+ $(NOECHO) $(TOUCH) pm_to_blib
+
+
+# --- MakeMaker selfdocument section:
+
+
+# --- MakeMaker postamble section:
+
+conf_install ::
+ $(PERL) "/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/install_util/conf_install.pl" "CGIBIN=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse/usr/lib/cgi-bin" "DO_XS=1" "APACHE=/usr/local/apache" "CONF=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse/etc/" "HTDOCS=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse/var/www"
+
+htdocs_install ::
+ $(PERL) "/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/install_util/htdocs_install.pl" "CGIBIN=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse/usr/lib/cgi-bin" "DO_XS=1" "APACHE=/usr/local/apache" "CONF=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse/etc/" "HTDOCS=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse/var/www"
+
+cgi_install ::
+ $(PERL) "/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/install_util/cgi_install.pl" "CGIBIN=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse/usr/lib/cgi-bin" "DO_XS=1" "APACHE=/usr/local/apache" "CONF=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse/etc/" "HTDOCS=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse/var/www"
+
+
+
+# End.
Added: trunk/packages/gbrowse/trunk/bin/load_genbank.pl
===================================================================
--- trunk/packages/gbrowse/trunk/bin/load_genbank.pl (rev 0)
+++ trunk/packages/gbrowse/trunk/bin/load_genbank.pl 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,197 @@
+#!/usr/bin/perl
+# $Id: load_genbank.PLS,v 1.5 2004/11/23 20:33:08 scottcain Exp $
+use strict;
+use Bio::DB::GFF;
+use Getopt::Long;
+
+=head1 NAME
+
+load_genbank.pl - Load a Bio::DB::GFF database from GENBANK files.
+
+=head1 SYNOPSIS
+
+ % load_genbank.pl -d genbank -f localfile.gb
+ % load_genbank.pl -d genbank -a AP003256
+
+NOTE: The script bp_genbank2gff.pl in the BioPerl distribution is the
+same as this script.
+
+=head1 DESCRIPTION
+
+This script loads a Bio::DB::GFF database with the features contained
+in a either a local genbank file or an accession that is fetched from
+genbank. Various command-line options allow you to control which
+database to load and whether to allow an existing database to be
+overwritten.
+
+This script currently only uses MySQL, though it is a proof-of-
+principle and could easily be extended to work with other RDMS
+that are supported by GFF through adaptors.
+
+=head1 COMMAND-LINE OPTIONS
+
+Command-line options can be abbreviated to single-letter options.
+e.g. -d instead of --database.
+
+ --create Force creation and initialization of database
+ --dsn <dsn> Data source (default dbi:mysql:test)
+ --user <user> Username for mysql authentication
+ --pass <password> Password for mysql authentication
+ --proxy <proxy> Proxy server to use for remote access
+ --file Arguments that follow are Genbank/EMBL file names (default)
+ --accession Arguments that follow are genbank accession numbers
+ --stdout Write converted GFF file to stdout rather than loading
+
+=head1 SEE ALSO
+
+L<Bio::DB::GFF>, L<bulk_load_gff.pl>, L<load_gff.pl>
+
+=head1 AUTHOR
+
+Scott Cain, cain at cshl.org
+
+Lincoln Stein, lstein at cshl.org
+
+Copyright (c) 2003 Cold Spring Harbor Laboratory
+
+This library is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself. See DISCLAIMER.txt for
+disclaimers of warranty.
+
+=cut
+
+package Bio::DB::GFF::Adaptor::biofetch_to_stdout;
+use CGI 'escape';
+use Bio::DB::GFF::Util::Rearrange;
+use Bio::DB::GFF::Adaptor::biofetch;
+use vars '@ISA';
+ at ISA = 'Bio::DB::GFF::Adaptor::biofetch';
+
+sub new {
+ my $class = shift;
+ my $self = bless {},$class;
+ my ($proxy) = rearrange(['PROXY'], at _);
+ if ($proxy) {
+ my @args = ref($proxy) ? @$proxy : eval $proxy;
+ $self->{_proxy} = \@args if @args;
+ }
+ $self;
+}
+
+sub load_gff_line {
+ my ($self,$options) = @_;
+ # synthesize GFF3-compatible line
+ my @attributes;
+ if (my $parent = $options->{gname}) {
+ push @attributes,"Parent=".escape($parent) unless $options->{method} =~ /^gene$/;
+ push @attributes,"ID=".escape($parent);
+ }
+ if (my $tstart = $options->{tstart}) {
+ my $tstop = $options->{tstop};
+ my $target = escape($options->{gname});
+ push @attributes,"Target=$target+$tstart+$tstop";
+ }
+ my %a;
+ if (my $attributes = $options->{attributes}) {
+ for my $a (@$attributes) {
+ my ($tag,$value) = @$a;
+ push @{$a{escape($tag)}},escape($value);
+ }
+ for my $a (keys %a) {
+ push @attributes,"$a=".join(',',@{$a{$a}});
+ }
+ }
+ my $last_column = join ';', at attributes;
+ if ($options->{method} eq 'origin') {
+ print "##sequence-region $options->{gname} $options->{start} $options->{stop}\n";
+ }
+ $$options{score} ||='.';
+ $$options{source} ||='genbank';
+ print join("\t",@{$options}{qw(ref source method start stop score strand phase)},$last_column),"\n";
+}
+
+sub load_sequence_string {
+ my $self = shift;
+ my ($acc,$seq) = @_;
+ $seq =~ s/(.{1,60})/$1\n/g;
+ print ">$acc\n\L$seq\U\n";
+}
+
+sub setup_load {
+ my $self = shift;
+ print "##gff-version 3\n";
+}
+
+sub finish_load { }
+
+1;
+
+package main;
+
+my ($DSN,$ADAPTOR,$CREATE,$USER,$PASSWORD,$FASTA,$ACC,$FILE,$PROXY,$STDOUT);
+
+GetOptions ('dsn:s' => \$DSN,
+ 'user:s' => \$USER,
+ 'password:s' => \$PASSWORD,
+ 'accession' => \$ACC,
+ 'file' => \$FILE,
+ 'proxy:s' => \$PROXY,
+ stdout => \$STDOUT,
+ create => \$CREATE) or die <<USAGE;
+Usage: $0 [options] <gff file 1> <gff file 2> ...
+Load a Bio::DB::GFF database from GFF files.
+
+ Options:
+ --create Force creation and initialization of database
+ --dsn <dsn> Data source (default dbi:mysql:test)
+ --user <user> Username for mysql authentication
+ --pass <password> Password for mysql authentication
+ --proxy <proxy> Proxy server to use for remote access
+ --file Arguments that follow are Genbank/EMBL file names (default)
+ --accession Arguments that follow are genbank accession numbers
+
+This script loads a Bio::DB::GFF database with the features contained
+in a either a local genbank file or an accession that is fetched from
+genbank. Various command-line options allow you to control which
+database to load and whether to allow an existing database to be
+overwritten.
+
+This script currently only uses MySQL, though it is a proof-of-
+principle and could easily be extended to work with other RDMS
+that are supported by GFF through adaptors.
+
+USAGE
+;
+
+# some local defaults
+$DSN ||= 'dbi:mysql:test';
+$ADAPTOR = $STDOUT ? 'biofetch_to_stdout' : 'biofetch';
+
+my @auth;
+push @auth,(-user=>$USER) if defined $USER;
+push @auth,(-pass=>$PASSWORD) if defined $PASSWORD;
+push @auth,(-proxy=>$PROXY) if defined $PROXY;
+
+my $db = Bio::DB::GFF->new(-adaptor=>$ADAPTOR,-dsn => $DSN, at auth)
+ or die "Can't open database: ",Bio::DB::GFF->error,"\n";
+
+if ($CREATE) {
+ $db->initialize(1);
+}
+
+die "you must specify either an accession to retrieve from\nembl or a local file containing data in embl format\n"
+ unless @ARGV;
+
+if ($ACC && !$FILE) {
+ while ($_ = shift) {
+ print STDERR "Loading $_...";
+ my $result = $db->load_from_embl(/^NC_/?'refseq':'embl' => $_);
+ print STDERR $result ? "ok\n" : "failed\n";
+ }
+} else {
+ while ($_ = shift) {
+ print STDERR "Loading $_...\n";
+ my $result = $db->load_from_file($_);
+ print STDERR $result ? "ok\n" : "failed\n";
+ }
+}
Added: trunk/packages/gbrowse/trunk/bin/make_das_conf.pl
===================================================================
--- trunk/packages/gbrowse/trunk/bin/make_das_conf.pl (rev 0)
+++ trunk/packages/gbrowse/trunk/bin/make_das_conf.pl 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,280 @@
+#!/usr/bin/perl
+# $Id: make_das_conf.PLS,v 1.2.6.1.2.1 2006/09/21 19:39:14 lstein Exp $
+
+use strict;
+use Bio::Das 1.03;
+use Getopt::Long;
+
+my @COLORS = qw(cyan blue red yellow green wheat turquoise orange); # default colors
+my $color = 0; # position in color cycle
+my %known_aggregators = map {$_=>1} qw(clone match processed_transcript wormbase_gene
+ orf reftranscript waba_alignment
+ coding cds alignment transcript
+ ucsc_assembly ucsc_ensgene ucsc_refgene
+ ucsc_sanger22 ucsc_sanger22pseudo
+ ucsc_softberry ucsc_twinscan ucsc_unigene);
+my $proxy;
+
+GetOptions('proxy=s' => \$proxy) or usage_statement();
+
+my $url = shift;
+$url or usage_statement();
+$url =~ m!^http:.+das(/\w+)?$! or usage_statement("This doesn't look like a DAS URL to me.");
+$ENV{HTTP_PROXY} ||= $proxy;
+
+list_sources($url) && exit 0 if $url =~ m!das/?$!;
+generate_config_file($url);
+
+exit 0;
+
+sub usage_statement {
+ my $error = shift;
+ $error .= "\n" if $error;
+
+die <<END;
+${error}Usage: $0 <das URL to load>
+
+Options: -proxy <http proxy to use>
+
+This utility attempts to contact a DAS source and to create a starter
+configuration file for gbrowse. If you don\'t know the list of data sources
+it will retrieve them and ask you to select one.
+
+If you need an HTTP proxy, set the HTTP_PROXY environment variable to
+the host and port number, in the form "http://proxy.host:port/", or
+pass the proxy URL to the -proxy option.
+END
+; }
+
+sub list_sources {
+ my $url = shift;
+ my $das = Bio::Das->new($url);
+ warn "proxy = $ENV{HTTP_PROXY}";
+ $das->proxy($ENV{HTTP_PROXY}) if $ENV{HTTP_PROXY};
+ my @sources = $das->sources or bad_request_exit($das);
+ print "The following DAS URLs are available at this server. Please call the script again\n";
+ print "using one of the following URLs:\n\n";
+ for my $s (@sources) {
+ print $s->url,"\n";
+ print "\t",$s->description,"\n\n";
+ }
+ 1;
+}
+
+sub generate_config_file {
+ my $url = shift;
+ my ($server,$dsn) = $url=~ m[^(.+/das)/(\w+)];
+ my $das = Bio::Das->new($server=>$dsn);
+
+ $das->proxy($ENV{HTTP_PROXY}) if $ENV{HTTP_PROXY};
+
+ my @sources = $das->sources or bad_request_exit($das);
+ my ($source) = grep {$_->id eq $das->default_dsn} @sources;
+
+ my @types = $das->types or bad_request_exit($das);
+ $source or bad_request_exit($das);
+
+ my %seenit;
+ my @aggregators = grep {!$seenit{$_}++}
+ map {
+ my ($method,$source) = split ':';
+ $known_aggregators{$method} ? $method : "$method\{$method\}"
+ } @types;
+ my $aggregators = join "\n ", at aggregators;
+
+ my $description = $source->description;
+ my $mapmaster = $source->master;
+ my @entry_points = sort {"$a" cmp "$b"} $das->entry_points;
+ foreach (@entry_points) { # remove coordinates
+ s/:\d+,\d+$//;
+ }
+
+ my $proxy = $ENV{HTTP_PROXY} ? "-proxy $ENV{HTTP_PROXY}" : '';
+
+ # top part of the config file
+ print <<END;
+[GENERAL]
+description = $description
+db_adaptor = Bio::Das
+db_args = -source $server
+ -dsn $dsn
+ $proxy
+
+# examples to show in the introduction
+examples = @entry_points
+
+das mapmaster = $mapmaster
+
+aggregators = $aggregators
+plugins =
+
+# list of tracks to turn on by default
+default features =
+
+# The class of the objects used to establish the reference coordinates.
+reference class = Sequence
+
+# "automatic" classes to try when an unqualified identifier is given
+automatic classes =
+
+# a footer
+footer = <hr>
+ <table width="100%">
+ <TR>
+ <TD align="LEFT" class="databody">
+ For the source code for this browser, see the <a href="http://www.gmod.org">
+ Generic Model Organism Database Project.</a> For other questions, send
+ mail to <a href="mailto:lstein\@cshl.org">lstein\@cshl.org</a>.
+ </TD>
+ </TR>
+ </table>
+ <hr>
+
+# Various places where you can insert your own HTML -- see configuration docs
+html1 =
+html2 =
+html3 =
+html4 =
+html5 =
+html6 =
+
+# what image widths to offer
+image widths = 450 640 800 1024
+
+# default width of detailed view (pixels)
+default width = 800
+
+# Web site configuration info
+stylesheet = /gbrowse/gbrowse.css
+buttons = /gbrowse/images/buttons
+tmpimages = /gbrowse/tmp
+
+# max and default segment sizes for detailed view
+max segment = 1000000
+default segment = 100000
+
+# zoom levels
+zoom levels = 100 200 1000 2000 5000 10000 20000 50000 100000 2000000 500000 1000000
+
+# colors of the overview, detailed map and key
+overview bgcolor = lightgrey
+detailed bgcolor = lightgoldenrodyellow
+key bgcolor = beige
+
+########################
+# Default glyph settings
+########################
+
+[TRACK DEFAULTS]
+glyph = segments
+height = 10
+bgcolor = lightgrey
+fgcolor = black
+font2color = blue
+label density = 25
+bump density = 100
+label = 1
+description = 1
+
+END
+;
+
+ for my $type (@types) {
+ my $method = $type->method || $type;
+ my $source = $type->source;
+ my $label = uc ($type eq $method ? $type : "${type}_${method}");
+ $label =~ s/:/_/g;
+ my $desc = $source ? "These are ${method} features from $source." : "These are ${method} features.";
+ my $key = $type;
+ my $category = $type->category;
+ my $idx = $color++ % @COLORS;
+ print <<END;
+[$label]
+feature = $type
+bgcolor = $COLORS[$idx]
+das category = $category
+key = $key
+citation = $desc
+
+END
+ }
+}
+
+sub bad_request_exit {
+ my $das = shift;
+ my $error = $das->error;
+ die <<END;
+$error
+
+An error was encountered while processing the DAS request. Are you sure this
+is an operational DAS server?
+END
+}
+
+# boilerplate
+__END__
+
+=head1 NAME
+
+make_das_conf.pl - Create GBrowse config files from DAS sources
+
+=head1 SYNOPSIS
+
+ % make_das_conf.pl http://genome.cse.ucsc.edu/cgi-bin/das/hg16 > /usr/local/apache/conf/gbrowse.conf/ucsc.conf
+
+=head1 DESCRIPTION
+
+This script generates a rough draft configuration file suitable for
+browsing a remote DAS server.
+
+To use this script, give it the URL of a DAS server. If you point it
+at the DAS base URL (without the data source name), as in
+"http://genome.cse.ucsc.edu/cgi-bin/das", it will print a list of
+valid data sources to standard output. If you give it a complete DAS
+URL, as in "http://genome.cse.ucsc.edu/cgi-bin/das/hg16", it will
+print a gbrowse configuration file to standard output.
+
+You will probably want to tweak the configuration file after you
+generate it. In particular, you will want to customize the glyph
+types associated with each track and adjust the list of examples given
+in the instructions (by default this script uses the complete list of
+entry points, which may be rather long).
+
+Also be aware that this script creates a set of aggregators that may
+or may not be correct. Consider the case of a DAS server which uses
+the canonical structure for a spliced mRNA:
+
+ main method: mRNA
+ subparts: 5'-UTR, CDS, 3'-UTR
+
+This conversion script will generate the following set of aggregators:
+
+ mRNA{mRNA}
+ 5'-UTR{5'-UTR}
+ CDS{CDS}
+ 3'-UTR{3'-UTR}
+
+It will also generate a total of four tracks, one each for the mRNA
+and each of its parts.
+
+This is, of course, incorrect. You will want to consolidate these into
+a single aggregator:
+
+ mRNA{5'-UTR,3'-UTR,CDS/mRNA}
+
+=head1 SEE ALSO
+
+L<Bio::DB::GFF>, L<bulk_load_gff.pl>, L<load_gff.pl>
+
+=head1 AUTHOR
+
+Lincoln Stein <lstein at cshl.org>.
+
+Copyright (c) 2002 Cold Spring Harbor Laboratory
+
+This library is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself. See DISCLAIMER.txt for
+disclaimers of warranty.
+
+=cut
+
Added: trunk/packages/gbrowse/trunk/bin/process_gadfly.pl
===================================================================
--- trunk/packages/gbrowse/trunk/bin/process_gadfly.pl (rev 0)
+++ trunk/packages/gbrowse/trunk/bin/process_gadfly.pl 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,194 @@
+#!/usr/bin/perl
+if ($ARGV[0]=~/^-?-h/ || @ARGV < 1) {
+die <<'USAGE';
+
+This script massages the RELEASE 3 Flybase/Gadfly GFF files located at
+http://www.fruitfly.org/sequence/release3download.shtml into the
+"correct" version of the GFF format.
+
+To use this script, download the whole genome FASTA file and save it
+to disk. (The downloaded file will be called something like
+"na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the
+HTML page doesn't give the filename.) Do the same for the whole
+genome GFF annotation file (the saved file will be called something
+like "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".) If
+you wish you can download the ZIP compressed versions of these files.
+
+Next run this script on the two files, indicating the name of the
+downloaded FASTA file first, followed by the gff file:
+
+ % process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
+
+The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database
+using the following command:
+
+ % bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff
+
+(Where "fly" is the name of the database. Change it as appropriate.
+The database must already exist and be writable by you!)
+
+The resulting database will have the following feature types
+(represented as "method:source"):
+
+ Component:arm A chromosome arm
+ Component:scaffold A chromosome scaffold (accession #)
+ Component:gap A gap in the assembly
+ clone:clonelocator A BAC clone
+ gene:gadfly A gene accession number
+ transcript:gadfly A transcript accession number
+ translation:gadfly A translation
+ codon:gadfly Significance unknown
+ exon:gadfly An exon
+ symbol:gadfly A classical gene symbol
+ similarity:blastn A BLASTN hit
+ similarity:blastx A BLASTX hit
+ similarity:sim4 EST->genome using SIM4
+ similarity:groupest EST->genome using GROUPEST
+ similarity:repeatmasker A repeat
+
+IMPORTANT NOTE: This script will *only* work with the RELEASE3 gadfly
+files and will not work with earlier releases.
+
+USAGE
+;
+}
+
+use strict;
+
+foreach (@ARGV) {
+ $_ = "gunzip -c $_ |" if /\.gz$/;
+}
+
+if ($ARGV[0] =~ /fasta/i) {
+ process_fasta();
+} else {
+ die "call as process_gadfly.pl \"release3_dna.FASTA\" \"release3_features.GFF\"";
+}
+
+while (<>) {
+ next if /^\#/;
+ chomp;
+ my ($ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,$cgroup) = split "\t";
+ next if $start > $stop; # something wrong. Don't bother fixing it.
+
+ my $fixed_group = fix_group($csource,$cmethod,$cgroup);
+ print join("\t",$ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,$fixed_group),"\n";
+ dump_symbol($ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,$cgroup) if $cgroup =~ /symbol/i;
+}
+
+sub fix_group {
+ my ($source,$method,$group) = @_;
+ my (@group,$gene);
+ push @group,"Transcript $1" if $group =~ /transgrp=([^; ]+)/;
+ push @group,"Gene $1" if $method eq 'gene' && $group =~ /genegrp=([^; ]+)/;
+
+ $gene ||= qq(Note "FlyBase $1") if $group =~ /dbxref=FlyBase:(\w+)/;
+ $gene ||= qq(Note "GadFly $1") if $group =~ /genegrp=([^; ]+)/;
+ push @group,qq(Note "Symbol $1") if $group =~ /symbol=([^; ]+)/ && "Gene $1" ne $group[0];
+ push @group,$gene;
+ return join ' ; ', at group;
+}
+
+# called when we encounter a gene symbol
+sub dump_symbol {
+ my ($ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,$cgroup) = @_;
+ my ($symbol) = $cgroup=~/symbol=([^;]+)/;
+ my ($gene) = $cgroup=~/genegrp=([^;]+)/;
+ return if $symbol eq $gene;
+ $cmethod = 'symbol';
+ print join("\t",$ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,qq(Symbol "$symbol")),"\n";
+}
+
+sub process_fasta {
+ my $file = shift @ARGV;
+ open F,$file or die "Can't open $file: $!";
+ print STDERR "Reading big FASTA file, please be patient...\n";
+ my ($current_id,%lengths);
+ while (<F>) {
+ if (/^>(\S+)/) {
+ $current_id = $1;
+ next;
+ }
+ die "this doesn't look like a fasta file to me" unless $current_id;
+ chomp;
+ $lengths{$current_id} += length;
+ }
+ foreach (sort keys %lengths) {
+ print join("\t",$_,'arm','Component',1,$lengths{$_},'.','+','.',qq(Sequence "$_")),"\n";
+ }
+}
+
+__END__
+
+=head1 NAME
+
+process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
+
+=head1 SYNOPSIS
+
+ % process_gadfly.pl ./RELEASE2 > gadfly.gff
+
+=head1 DESCRIPTION
+
+This script massages the RELEASE 3 Flybase/Gadfly GFF files located at
+http://www.fruitfly.org/sequence/release3download.shtml into the "correct"
+version of the GFF format.
+
+To use this script, download the whole genome FASTA file and save it
+to disk. (The downloaded file will be called something like
+"na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the
+HTML page doesn't give the filename.) Do the same for the whole
+genome GFF annotation file (the saved file will be called something
+like "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".) If
+you wish you can download the ZIP compressed versions of these files.
+
+Next run this script on the two files, indicating the name of the
+downloaded FASTA file first, followed by the gff file:
+
+ % process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
+
+The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database
+using the following command:
+
+ % bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff
+
+(Where "fly" is the name of the database. Change it as appropriate.
+The database must already exist and be writable by you!)
+
+The resulting database will have the following feature types
+(represented as "method:source"):
+
+ Component:arm A chromosome arm
+ Component:scaffold A chromosome scaffold (accession #)
+ Component:gap A gap in the assembly
+ clone:clonelocator A BAC clone
+ gene:gadfly A gene accession number
+ transcript:gadfly A transcript accession number
+ translation:gadfly A translation
+ codon:gadfly Significance unknown
+ exon:gadfly An exon
+ symbol:gadfly A classical gene symbol
+ similarity:blastn A BLASTN hit
+ similarity:blastx A BLASTX hit
+ similarity:sim4 EST->genome using SIM4
+ similarity:groupest EST->genome using GROUPEST
+ similarity:repeatmasker A repeat
+
+IMPORTANT NOTE: This script will *only* work with the RELEASE3 gadfly
+files and will not work with earlier releases.
+
+=head1 SEE ALSO
+
+L<Bio::DB::GFF>, L<bulk_load_gff.pl>, L<load_gff.pl>
+
+=head1 AUTHOR
+
+Lincoln Stein <lstein at cshl.org>.
+
+Copyright (c) 2002 Cold Spring Harbor Laboratory
+
+This library is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself. See DISCLAIMER.txt for
+disclaimers of warranty.
+
+=cut
Added: trunk/packages/gbrowse/trunk/bin/process_sgd.pl
===================================================================
--- trunk/packages/gbrowse/trunk/bin/process_sgd.pl (rev 0)
+++ trunk/packages/gbrowse/trunk/bin/process_sgd.pl 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,126 @@
+#!/usr/bin/perl
+
+# $Id: process_sgd.PLS,v 1.2 2002/02/18 22:47:34 lstein Exp $
+# This script will convert from SGD format to GFF format
+# See http://genome-www4.stanford.edu/Saccharomyces/SGD/doc/db_specifications.html
+
+use strict;
+
+# hard-coded length data that I couldn't get directly
+my %CHROMOSOMES = (I => 230_203,
+ II => 813_139,
+ III => 316_613,
+ IV => 1_531_929,
+ V => 576_869,
+ VI => 270_148,
+ VII => 1_090_937,
+ VIII => 562_639,
+ IX => 439_885,
+ X => 745_444,
+ XI => 666_445,
+ XII => 1_078_173,
+ XIII => 924_430,
+ XIV => 784_328,
+ XV => 1_091_284,
+ XVI => 948_061,
+ Mit => 85_779);
+my @ROMAN = qw(I II III IV V VI VII VIII IX X
+ XI XII XIII XIV XV XVI Mit);
+
+if ($ARGV[0] =~ /^--?h/) {
+ die <<USAGE;
+ Usage: $0 <SGD features file>
+
+This script massages the SGD sequence annotation flat files located at
+ftp://genome-ftp.stanford.edu/pub/yeast/data_dump/feature/chromosomal_features.tab
+into a version of the GFF format suitable for display by the generic
+genome browser.
+
+To use this script, get the SGD chromosomal_features.tab file from the
+FTP site listed above, and run the following command:
+
+ % process_sgd.pl chromosomal_features.tab > yeast.gff
+
+The yeast.gff file can then be loaded into a Bio::DB::GFF database
+using the following command:
+
+ % bulk_load_gff.pl -d <databasename> yeast.gff
+
+USAGE
+;
+}
+
+# first print out chromosomes
+# We hard coded the lengths because they are not available in the features table.
+for my $chrom (sort keys %CHROMOSOMES) {
+ print join("\t",$chrom,'chromosome','Component',1,$CHROMOSOMES{$chrom},'.','.','.',qq(Sequence "$chrom")),"\n";
+}
+
+# this is hard because the SGD idea of a feature doesn't really map onto the GFF idea.
+while (<>) {
+ chomp;
+ my($id,$gene,$aliases,$type,$chromosome,$start,$stop,$strand,$sgdid,$sgdid2,$description,$date) = split "\t";
+ my $ref = $ROMAN[$chromosome-1];
+ $description =~ s/"/\\"/g;
+ $description =~ s/;/\\;/g;
+
+ $strand = $strand eq 'W' ? '+' : '-';
+ ($start,$stop) = ($stop,$start) if $strand eq '-';
+ die "Strand logic is messed up" if $stop < $start;
+
+ if ($gene) {
+ my @aliases = split(/\|/,$aliases);
+ my $aliases = join " ; ",map {qq(Alias "$_")} @aliases;
+ my $group = qq(Gene "$gene" ; Note "$description");
+ $group .= " ; $aliases" if $aliases;
+ print join("\t",$ref,'sgd','gene',$start,$stop,'.',$strand,'.',$group),"\n";
+ $description .= "\\; AKA @aliases" if @aliases;
+ }
+
+ print join("\t",$ref,'sgd',$type,$start,$stop,'.',$strand,'.',qq($type "$id" ; Note "$description")),"\n";
+}
+
+__END__
+
+=head1 NAME
+
+process_sgd.pl - Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
+
+=head1 SYNOPSIS
+
+ % process_sgd.pl chromosomal_features.tab > yeast.gff
+
+=head1 DESCRIPTION
+
+This script massages the SGD sequence annotation flat files located at
+ftp://genome-ftp.stanford.edu/pub/yeast/data_dump/feature/chromosomal_features.tab
+into a version of the GFF format suitable for display by the generic
+genome browser.
+
+To use this script, get the SGD chromosomal_features.tab file from the
+FTP site listed above, and run the following command:
+
+ % process_sgd.pl chromosomal_features.tab > yeast.gff
+
+The yeast.gff file can then be loaded into a Bio::DB::GFF database
+using the following command:
+
+ % bulk_load_gff.pl -d <databasename> yeast.gff
+
+=head1 SEE ALSO
+
+L<Bio::DB::GFF>, L<bulk_load_gff.pl>, L<load_gff.pl>
+
+=head1 AUTHOR
+
+Lincoln Stein <lstein at cshl.org>.
+
+Copyright (c) 2002 Cold Spring Harbor Laboratory
+
+This library is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself. See DISCLAIMER.txt for
+disclaimers of warranty.
+
+=cut
+
+
Added: trunk/packages/gbrowse/trunk/bin/process_wormbase.pl
===================================================================
--- trunk/packages/gbrowse/trunk/bin/process_wormbase.pl (rev 0)
+++ trunk/packages/gbrowse/trunk/bin/process_wormbase.pl 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,251 @@
+#!/usr/bin/perl
+
+use constant ACEDB => 'sace://aceserver.cshl.org:2005';
+use strict;
+use Ace;
+
+my @framework = qw(mex-3 spe-15 lin-17 unc-11 dhc-1 unc-40 smg-5
+ unc-13 unc-29 eat-16 lin-11 spe-9 par-6 unc-59 unc-54 mab-9 lin-42
+ sri-71 smu-2 vab-1 bli-2 dpy-10 him-14 mig-5 unc-4 bli-1 sqt-1 rol-1
+ his-14 unc-52 unc-45 par-2 let-805 sel-8 mab-21 daf-4 sma-3 lin-39
+ unc-32 tax-4 ced-9 tra-1 nob-1 daf-1 ced-2 lin-1 unc-17 dpy-13 unc-5
+ smg-7 dif-1 lin-49 elt-1 daf-14 dpy-20 dpy-26 unc-30 tra-3 sup-24
+ rho-1 egl-8 unc-60 srh-36 apx-1 unc-62 let-418 dpy-11 let-413 sel-9
+ unc-42 egl-9 sma-1 sqt-3 odr-3 hda-1 unc-76 gcy-20 skr-5 par-4 unc-51
+ egl-17 lim-6 fox-1 fax-1 lon-2 unc-97 unc-6 unc-18 mec-10 sop-1 mab-18
+ sdc-2 odr-7 unc-9 unc-3 gas-1 ace-1);
+my %framework = map {$_=>1} @framework;
+my %framework_seen = ();
+
+my $USAGE = <<USAGE;
+This script massages the Wormbase GFF files located at
+ftp://www.wormbase.org/pub/wormbase/GENE_DUMPS into a version of the
+GFF format suitable for display by the generic genome browser. It
+mainly adds comments to the annotations and designates certain
+well-spaced genetic loci as framework landmarks.
+
+This script requires the AcePerl distribution, which is available on
+CPAN (look for the "Ace" module).
+
+To use this script, get the WormBase GFF files from the FTP site
+listed above and place them in a directory. It might be a good idea
+to name the directory after the current release, such as WS61. You do
+not need to uncompress the files.
+
+Then give that directory as the argument to this script and capture
+the script's output to a file:
+
+ % process_wormbase.pl ./WS61 > wormbase.gff
+
+It may take a while before you see output from this script, since it
+must first fetch gene and protein database from the remote AceDB
+running at www.wormbase.org.
+The wormbase.gff file can then be loaded into a Bio::DB::GFF database
+using the following command:
+
+ % bulk_load_gff.pl -d <databasename> wormbase.gff
+USAGE
+;
+#'
+
+die $USAGE if $ARGV[0]=~/^-?-h/i;
+
+my $db = Ace->connect(-url=>ACEDB,
+ -query_timeout=>500) or die "Can't open ace database:",Ace->error;
+
+if (-d $ARGV[0]) {
+ @ARGV = <$ARGV[0]/*.gff.gz>;
+}
+
+ at ARGV || die $USAGE;
+
+foreach (@ARGV) { # GFF FILES
+ $_ = "gunzip -c $_ |" if /\.gz$/;
+}
+
+my (%NOTES,%LOCUS,%GENBANK,%CONFIRMED,%ORFEOME);
+get_confirmed($db,\%CONFIRMED);
+get_genbank($db,\%GENBANK);
+get_loci($db,\%LOCUS);
+get_transcripts($db,\%LOCUS);
+get_notes($db,\%NOTES);
+get_orfeome($db,\%ORFEOME);
+
+while (<>) {
+ chomp;
+ next if /^\#/;
+ my ($ref,$source,$method,$start,$stop,$score,$strand,$phase,$group) = split /\t/;
+ next if $source eq 'assembly_tag'; # don't want 'em, don't need 'em
+ next if $method eq 'HOMOL_GAP'; # don't want that neither
+ $ref =~ s/^CHROMOSOME_//;
+ $group =~ s/CHROMOSOME_//;
+
+ $source ='' if $source eq '*UNKNOWN*';
+
+ if ($method =~ /Transcript|CDS/
+ && ($source =~ /curated|RNA|miRNA/)
+ && $group =~ /Transcript|CDS "(\w+\.\d+[a-z]?)"/) {
+ my @notes;
+ push @notes,map { qq(Note "$_") } @{$NOTES{$1}} if $NOTES{$1};
+ push @notes,map { qq(Note "$_") } @{$LOCUS{$1}} if $LOCUS{$1};
+ push @notes,qq(Confirmed_by "$CONFIRMED{$1}") if $CONFIRMED{$1};
+ $group = join ' ; ',$group, at notes;
+ if (my $loci = $LOCUS{$1}) {
+ foreach (@$loci) {
+ print join("\t",$ref,$source,'gene',$start,$stop,$score,$strand,$phase,"Locus $_"),"\n";
+ print join("\t",$ref,'framework','gene',$start,$stop,$score,$strand,$phase,"Locus $_"),"\n"
+ if $framework{$_} && !$framework_seen{$_}++;
+ }
+ }
+ }
+
+ if ($method eq 'region' && $source eq 'Genomic_canonical' && $group =~ /Sequence "(\w+)"/) {
+ if (my $accession = $GENBANK{$1}) {
+ $group .= qq( ; Note "Genbank $accession");
+ print join("\t",$ref,'Genbank',$method,$start,$stop,$score,$strand,$phase,"Genbank \"$accession\""),"\n";
+ }
+ }
+
+ if ($method eq 'intron' && $source =~ /^tRNAscan/) {
+ next; # messing up tRNA scanning
+ }
+
+ if ($method eq 'PCR_product' && $source eq 'Orfeome' && $group =~ /PCR_product "([^\"]+)"/) {
+ my $amp = $ORFEOME{$1};
+ $group .= qq( ; Amplified $amp) if defined $amp;
+ }
+
+ # fix variant fields: Variant "T" => Note "T"
+ $group =~ s/(?:Variant|Insert) "(\w+)"/Note "$1"/;
+
+ # fix UTR fields
+ if ($group =~ /UTR "([35])_UTR:(\S+)"/) {
+ $method = 'UTR';
+ $source = "curated";
+ $group = qq(CDS "$2");
+ }
+
+ print join("\t",$ref,$source,$method,$start,$stop,$score,$strand,$phase,$group),"\n";
+}
+
+sub get_loci {
+ my ($db,$hash) = @_; # hash keys are predicted gene names, values are one or more loci names
+ my @genes = $db->fetch(-query=>'find Locus CDS',-filltag=>'CDS');
+ foreach my $obj (@genes) {
+ my @genomic = $obj->CDS or next;
+ foreach (@genomic) {
+ push @{$hash->{$_}},$obj;
+ }
+ }
+}
+
+sub get_transcripts {
+ my ($db,$hash) = @_; # hash keys are predicted gene names, values are one or more loci names
+ my @genes = $db->fetch(-query=>'find Locus Transcript',-filltag=>'Transcript');
+ foreach my $obj (@genes) {
+ my @genomic = $obj->Transcript or next;
+ foreach (@genomic) {
+ push @{$hash->{$_}},$obj;
+ }
+ }
+}
+
+sub get_notes {
+ my ($db,$hash) = @_; # hash keys are predicted gene names, values are one or more brief identifications
+ my @genes = $db->fetch(-query=>'find CDS Brief_identification',-filltag=>'Brief_identification');
+ # Should probably also look for notes attached to sequences, yes? As before...
+ push (@genes,$db->fetch(-query=>'find Sequence Brief_identification',-filltag=>'Brief_identification'));
+ foreach my $obj (@genes) {
+ my @notes = $obj->Brief_identification or next;
+ $hash->{$obj} = \@notes;
+ }
+}
+
+sub get_genbank {
+ my ($db,$hash) = @_; # hash keys are cosmid names, values are genbank accessions (1 to 1)
+ my @cosmids = $db->fetch(-query=>'find Genome_Sequence Database',-filltag=>'Database');
+ for my $cosmid (@cosmids) {
+ my @dbs = $cosmid->Database;
+ foreach (@dbs) {
+ foreach my $col ($_->col) {
+ next unless $col eq 'NDB_AC';
+ $hash->{$cosmid} = $col->right;
+ }
+ }
+ }
+}
+
+sub get_confirmed {
+ my ($db,$hash) = @_; # hash keys are predicted gene names, values are confirmation type
+ my @confirmed = $db->fetch(-query=>'find Sequence Confirmed_by',-filltag=>'Confirmed_by');
+ foreach my $obj (@confirmed) {
+ my $confirmed_by = $obj->Confirmed_by || 'Unknown';
+ $hash->{$obj} = $confirmed_by;
+ }
+}
+
+sub get_orfeome {
+ my ($db,$hash) = @_;
+ my @mv_primers = $db->fetch(-query=>'find PCR_Product mv*',-filltag=>'Amplified');
+ for my $obj (@mv_primers) {
+ my $amplified = $obj->Amplified;
+ $hash->{$obj} = $amplified;
+ }
+}
+
+__END__
+
+=head1 NAME
+
+process_wormbase.pl - Massage WormBase GFF files into a version suitable for the Generic Genome Browser
+
+=head1 SYNOPSIS
+
+ % process_wormbase.pl ./WS121 > wormbase.gff
+
+=head1 DESCRIPTION
+
+This script massages the Wormbase GFF files located at
+ftp://www.wormbase.org/pub/wormbase/GENE_DUMPS into a version of the
+GFF format suitable for display by the generic genome browser. It is
+current for data releases WS121 and beyond. It mainly adds comments to
+the annotations and designates certain well-spaced genetic loci as
+framework landmarks.
+
+This script requires the AcePerl distribution, which is available on
+CPAN (look for the "Ace" module).
+
+To use this script, get the WormBase GFF files from the FTP site
+listed above and place them in a directory. It might be a good idea
+to name the directory after the current release, such as WS61. You do
+not need to uncompress the files.
+
+Then give that directory as the argument to this script and capture
+the script's output to a file:
+
+ % process_wormbase.pl ./WS121 > wormbase.gff
+
+It may take a while before you see output from this script, since it
+must first fetch gene and protein database from the remote AceDB
+running at www.wormbase.org.
+The wormbase.gff file can then be loaded into a Bio::DB::GFF database
+using the following command:
+
+ % bulk_load_gff.pl -d <databasename> wormbase.gff
+
+=head1 SEE ALSO
+
+L<Bio::DB::GFF>, L<bulk_load_gff.pl>, L<load_gff.pl>
+
+=head1 AUTHOR
+
+Lincoln Stein <lstein at cshl.org>.
+
+Copyright (c) 2002 Cold Spring Harbor Laboratory
+
+This library is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself. See DISCLAIMER.txt for
+disclaimers of warranty.
+
+=cut
+
Added: trunk/packages/gbrowse/trunk/bin/register_moby_services.pl
===================================================================
--- trunk/packages/gbrowse/trunk/bin/register_moby_services.pl (rev 0)
+++ trunk/packages/gbrowse/trunk/bin/register_moby_services.pl 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,335 @@
+#!/usr/bin/perl -w
+package MobyServices::GbrowseServices;
+
+###################################################################
+# Non-modperl users should change this variable if needed to point
+# to the directory in which the configuration files are stored.
+#
+$CONF_DIR = '/home/charles/src/gbrowse-1.68/debian/gbrowse/etc//gbrowse.conf';
+#
+###################################################################
+
+
+
+#=======================================================================
+#$Id: register_moby_services.PLS,v 1.5 2004/01/07 22:21:49 markwilkinson Exp $
+
+use MOBY::Client::Central;
+use strict;
+use Text::Shellwords;
+use MOBY::CommonSubs qw{:all};
+use Bio::Graphics::Browser;
+use Bio::Graphics::Browser::Util;
+
+use vars qw(%dbh $CONFIG $authURI $CONF_DIR $CGIDIR);
+
+if ($ARGV[0] && $ARGV[0] =~ /clean/){
+ &DEREGISTER_SERVICES();
+ print "services deregistered\n";
+ exit 1;
+} elsif ($ARGV[0] && $ARGV[0] =~ /register/){
+ ®ISTER_SERVICES();
+ print "services registered\n";
+ exit 1;
+} else {
+ print <<USAGE;
+
+usage: perl register_moby_services.pl -register (to register services)
+ perl register_moby_services.pl -clean (to deregister them)
+
+USAGE
+exit 0;
+}
+
+®ISTER_SERVICES() || die "Registration of your services failed for unknown reasons\n\n";
+
+exit 1;
+
+
+sub REGISTER_SERVICES {
+ _settings();
+ system 'clear';
+ print STDOUT "
+You MUST have configured the moby.conf file in your
+./gbrowse.conf/MobyServices folder to reflect your
+own server settings BEFORE you run this registration script!\n\n";
+
+ print STDOUT "Have you done this? [N/y]: ";
+ my $resp = <STDIN>;
+ chomp $resp;
+ die "
+Please go ahead and configure this file, then run this script again
+ " unless ($resp =~ /y/i);
+
+ open (DONE, ">>registeredMOBYServices.dat") || die "can't open the logfile registeredMOBYServices.dat to record the services you have registered in MOBY Central.\n";
+ my $C = MOBY::Client::Central->new();
+
+ # ======== get configuration settings from
+ # ======== the gbrowse/MobyServices/moby.conf
+ # ======== file, as well as the 0X.DBNAME.conf
+ # =============================================
+ my $reference = $CONFIG->{'MOBY'}->{'Reference'};
+ $reference = shift(@$reference); $reference ||='';
+
+ my $authURI = $CONFIG->{'MOBY'}->{'authURI'};
+ $authURI = shift(@$authURI); $authURI ||='unknown.org';
+
+ my $contactEmail = $CONFIG->{'MOBY'}->{'contactEmail'};
+ $contactEmail = shift(@$contactEmail);
+ die "\nYou have not configured a valid contactEmail parameter in
+ your config file!\n" unless ($contactEmail =~ /\S+\@\S+\.\S+/);
+
+ my $cgiURL = $CONFIG->{'MOBY'}->{'CGI_URL'};
+ $cgiURL = shift(@$cgiURL);
+ die "\nYou have not configured a valid CGI_URL parameter in
+ your config file!\n" unless ($cgiURL =~ "^http\://");
+
+ my @sources = $CONFIG->sources;
+
+ my @featureNamespaces = keys %{$CONFIG->{'MOBY'}->{'NAMESPACE'}};
+ # =============================================
+ # =============================================
+
+ my $description = "Consumes base Object's in the $reference namespace and does a retrieval of that sequence record from the ".(join ",", @sources)." database(s), returning it as a FASTA sequence object.";
+ my $success = TEST($C->registerService(
+ serviceName => "GbrowseGetReferenceFasta",
+ serviceType => "Retrieval",
+ authURI => $authURI,
+ contactEmail => $contactEmail,
+ description => $description,
+ category => "moby",
+ URL => "$cgiURL/moby_server",
+ input =>[
+ ['', ['Object', [$reference]]], # this will fail if the $reference namespace is not yet registered
+ ],
+ output =>[
+ ['', ['FASTA', [$reference]]],
+ ],
+ ), 1, 1);
+ unless ($success){
+ close DONE;
+ DEREGISTER_SERVICES();
+ die "registered services have been deregistered pending successful completion of this routine\n You will need to start again.\n";;
+ } else {
+ print DONE "$authURI\tGbrowseGetReferenceFasta\n";
+ }
+
+ $description = "Consumes base Object's in the $reference namespace and does a retrieval of that sequence record from the ".(join ",", @sources)." database(s), returning it as a GenericSequence object or better (i.e. DNASequence, RNASequence, or AminoAcidSequence).";
+ $success = TEST($C->registerService(
+ serviceName => "GbrowseGetReferenceSeqObj",
+ serviceType => "Retrieval",
+ authURI => $authURI,
+ contactEmail => $contactEmail,
+ description => $description,
+ category => "moby",
+ URL => "$cgiURL/moby_server",
+ input =>[
+ ['', ['Object', [$reference]]], # this will fail if the $reference namespace is not yet registered
+ ],
+ output =>[
+ ['', ['GenericSequence', [$reference]]],
+ ],
+ ), 1, 1);
+ unless ($success){
+ close DONE;
+ DEREGISTER_SERVICES();
+ die "registered services have been purged from MOBY Central pending successful completion of this routine\n You will need to start again.\n";;
+ } else {
+ print DONE "$authURI\tGbrowseGetReferenceSeqObj\n";
+ }
+
+
+ $description = "Consumes base Object's in the $reference namespace and does a retrieval of GFF2-formatted text from the ".(join ",", @sources)." database(s), returning it as a GFF2 object.";
+ $success = TEST($C->registerService(
+ serviceName => "GbrowseGetReferenceGFF2",
+ serviceType => "Retrieval",
+ authURI => $authURI,
+ contactEmail => $contactEmail,
+ description => $description,
+ category => "moby",
+ URL => "$cgiURL/moby_server",
+ input =>[
+ ['', ['Object', [$reference]]], # this will fail if the $reference namespace is not yet registered
+ ],
+ output =>[
+ ['', ['GFF2', [$reference]]],
+ ],
+ ), 1, 1);
+ unless ($success){
+ close DONE;
+ DEREGISTER_SERVICES();
+ die "registered services have been purged from MOBY Central pending successful completion of this routine\n You will need to start again.\n";;
+ } else {
+ print DONE "$authURI\tGbrowseGetReferenceSeqObj\n";
+ }
+
+
+ $description = "Consumes base Object's in the $reference namespace and does a retrieval of GFF3-formatted text plus FASTA from the ".(join ",", @sources)." database(s), returning it as a GFF3 object.";
+ $success = TEST($C->registerService(
+ serviceName => "GbrowseGetReferenceGFF3",
+ serviceType => "Retrieval",
+ authURI => $authURI,
+ contactEmail => $contactEmail,
+ description => $description,
+ category => "moby",
+ URL => "$cgiURL/moby_server",
+ input =>[
+ ['', ['Object', [$reference]]], # this will fail if the $reference namespace is not yet registered
+ ],
+ output =>[
+ ['', ['GFF3', [$reference]]],
+ ],
+ ), 1, 1);
+ unless ($success){
+ close DONE;
+ DEREGISTER_SERVICES();
+ die "registered services have been purged from MOBY Central pending successful completion of this routine\n You will need to start again.\n";;
+ } else {
+ print DONE "$authURI\tGbrowseGetReferenceSeqObj\n";
+ }
+
+ $description = "Consumes base Object's in the ".(join ",", @featureNamespaces)." namespace(s) and does a retrieval of GFF2-formatted text plus FASTA from the ".(join ",", @sources)." database(s), returning it as a GFF2 object.";
+ $success = TEST($C->registerService(
+ serviceName => "GbrowseGetFeatureGFF2",
+ serviceType => "Retrieval",
+ authURI => $authURI,
+ contactEmail => $contactEmail,
+ description => $description,
+ category => "moby",
+ URL => "$cgiURL/moby_server",
+ input =>[
+ ['', ['Object', \@featureNamespaces]], # this will fail if the $reference namespace is not yet registered
+ ],
+ output =>[
+ ['', ['GFF2', \@featureNamespaces]],
+ ],
+ ), 1, 1);
+ unless ($success){
+ close DONE;
+ DEREGISTER_SERVICES();
+ die "registered services have been purged from MOBY Central pending successful completion of this routine\n You will need to start again.\n";;
+ } else {
+ print DONE "$authURI\tGbrowseGetFeatureGFF2\n";
+ }
+
+
+ $description = "Consumes base Object's in the ".(join ",", @featureNamespaces)." namespace(s) and does a retrieval of GFF3-formatted text plus FASTA from the ".(join ",", @sources)." database(s), returning it as a GFF3 object.";
+ $success = TEST($C->registerService(
+ serviceName => "GbrowseGetFeatureGFF3",
+ serviceType => "Retrieval",
+ authURI => $authURI,
+ contactEmail => $contactEmail,
+ description => $description,
+ category => "moby",
+ URL => "$cgiURL/moby_server",
+ input =>[
+ ['', ['Object', \@featureNamespaces]], # this will fail if the $reference namespace is not yet registered
+ ],
+ output =>[
+ ['', ['GFF3', \@featureNamespaces]],
+ ],
+ ), 1, 1);
+ unless ($success){
+ close DONE;
+ DEREGISTER_SERVICES();
+ die "registered services have been purged from MOBY Central pending successful completion of this routine\n You will need to start again.\n";;
+ } else {
+ print DONE "$authURI\tGbrowseGetFeatureGFF3\n";
+ }
+
+
+ $description = "Consumes base Object's in the ".(join ",", @featureNamespaces)." namespace(s) and does a retrieval of a GenericSequence object or better (RNA, DNA, or AminoAcid Sequence) from the ".(join ",", @sources)." database(s).";
+ $success = TEST($C->registerService(
+ serviceName => "GbrowseGetFeatureSequenceObject",
+ serviceType => "Retrieval",
+ authURI => $authURI,
+ contactEmail => $contactEmail,
+ description => $description,
+ category => "moby",
+ URL => "$cgiURL/moby_server",
+ input =>[
+ ['', ['Object', \@featureNamespaces]], # this will fail if the $reference namespace is not yet registered
+ ],
+ output =>[
+ ['', ['GFF3', \@featureNamespaces]],
+ ],
+ ), 1, 1);
+ unless ($success){
+ close DONE;
+ DEREGISTER_SERVICES();
+ die "registered services have been purged from MOBY Central pending successful completion of this routine\n You will need to start again.\n";;
+ } else {
+ print DONE "$authURI\tGbrowseGetFeatureSequenceObject\n";
+ }
+
+
+ return 1;
+}
+
+sub DEREGISTER_SERVICES {
+ my $C = MOBY::Client::Central->new();
+ open (DONE, "registeredMOBYServices.dat") || die "can't open the logfile registeredMOBYServices.dat to get a listing of the services you have registered in MOBY Central.\n";
+ while (<DONE>){
+ chomp;
+ my ($auth, $name) = (($_=~/(\S+)\t(\S+)/) && ($1, $2));
+ ($auth && $name) || die "\n\n********** CORRUPT registeredMOBYServices.dat file *************\n non-recoverable error.";
+ my $success = TEST($C->deregisterService(
+ serviceName => $name,
+ authURI => $auth,
+ ), 2, 1);
+ }
+ close DONE;
+ open (DONE, ">registeredMOBYServices.dat") || die "can't open the logfile registeredMOBYServices.dat to purge list of registered services\n";
+ close DONE;
+}
+
+sub _settings {
+ $CONF_DIR = conf_dir($CONF_DIR); # conf_dir() is exported from Util.pm
+
+ ## CONFIGURATION & INITIALIZATION ################################
+ # preliminaries -- read and/or refresh the configuration directory
+ $CONFIG = open_config($CONF_DIR); # open_config() is exported from Util.pm
+ my @sources = $CONFIG->sources; # get all data sources
+
+ foreach (@sources){ # grab the database handle for each source
+ $CONFIG->source($_);
+ my $db = open_database($CONFIG);
+ $dbh{$_}=$db;
+ }
+
+ open (IN, "$CONF_DIR/MobyServices/moby.conf") || die "\n**** GbrowseServices.pm couldn't open configuration file $CONF_DIR/MobyServices/moby.conf: $!\n";
+ while (<IN>){
+ chomp; next unless $_; # filter out blank lines
+ next if m/^#/; # filter out comment lines
+ last if $_ =~ /\[Namespace_Class_Mappings\]/;
+ my @res = shellwords($_); # parse the tokens key = value1 value2 value3
+ $CONFIG->{MOBY}->{$res[0]} = [@res[2..scalar(@res)]]; # add them to the existing config with a new tag MOBY in key = \@values format
+ }
+ while (<IN>){ # now process the namespace mappings
+ chomp; next unless $_; # filter out blank lines
+ next if m/^#/; # filter out comment lines
+ my @res = shellwords($_); # parse the tokens key = value1 value2 value3
+ $CONFIG->{'MOBY'}->{'NAMESPACE'}->{$res[0]} = [$res[2]]; # add them to the existing config with a new tag MOBY in key = \@values format
+ }
+}
+
+
+sub TEST { # test of Registration object
+ my ($reg, $test, $expect) = @_;
+ die "\a\a\aREG OBJECT MALFORMED" unless $reg;
+ if ($reg->success == $expect){
+ print "test $test\t\t[PASS]\n";
+ return 1;
+ } else {
+ print "test $test\t\t[FAIL]\n",$reg->message,"\n\n";
+ return 0;
+ }
+
+}
+
+
+
+#=======================================================================
+
+
+
Added: trunk/packages/gbrowse/trunk/bin/ucsc_genes2gff.pl
===================================================================
--- trunk/packages/gbrowse/trunk/bin/ucsc_genes2gff.pl (rev 0)
+++ trunk/packages/gbrowse/trunk/bin/ucsc_genes2gff.pl 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,283 @@
+#!/usr/bin/perl
+
+# convert UCSC gene files into GFF3 data
+
+use strict;
+use File::Basename 'basename';
+use Getopt::Long;
+
+my $executable = basename($0);
+
+my ($SRC,$ORIGIN);
+GetOptions('src:s' => \$SRC,
+ 'origin:i' => \$ORIGIN,
+ ) or die <<USAGE;
+Usage: $0 [options] ucsc_file1 ucsc_file2...
+
+Convert UCSC Genome Browser-format gene files into GFF3 version files.
+Only the gene IDs and their locations come through. You have to get
+the comments and aliases some other way.
+
+Options:
+
+ -src <string> Choose a source for the gene, default "UCSC"
+ -origin <integer> Choose a relative position to number from, default is "1"
+
+The resulting file is in GFF3 format and should be loaded into a
+Bio::DB::GFF database using the following command:
+
+ bp_bulk_load_gff.pl -c -d db1 --maxfeature 1000000000 --gff3_munge file.gff
+
+USAGE
+
+$SRC ||= 'UCSC';
+$ORIGIN ||= 1;
+
+print "##gff-version 3\n";
+
+# automatically uncompress varous compression formats
+foreach (@ARGV) {
+ $_ = "gunzip -c $_ |" if /\.gz$/;
+ $_ = "uncompress -c $_ |" if /\.Z$/;
+ $_ = "bunzip2 -c $_ |" if /\.bz2$/;
+}
+
+while (<>) {
+ chomp;
+ next if /^\#/;;
+ next if /random/; ## added line
+ my
+($id,$chrom,$strand,$txStart,$txEnd,$cdsStart,$cdsEnd,$exons,$exonStarts,$exonEnds)
+= split /\t/;
+ my ($utr5_start,$utr5_end,$utr3_start,$utr3_end);
+
+ # adjust for Jim's 0-based coordinates
+ $txStart++;
+ $cdsStart++;
+
+ $txStart -= $ORIGIN;
+ $txEnd -= $ORIGIN;
+ $cdsStart -= $ORIGIN;
+ $cdsEnd -= $ORIGIN;
+
+ # print the transcript
+ print join
+("\t",$chrom,$SRC,'mRNA',$txStart,$txEnd,'.',$strand,'.',"ID=$id"),"\n";
+
+ # now handle the CDS entries -- the tricky part is the need to keep
+ # track of phase
+ my $phase = 0;
+ my @exon_starts = map {$_-$ORIGIN} split ',',$exonStarts;
+ my @exon_ends = map {$_-$ORIGIN} split ',',$exonEnds;
+
+
+ if ($strand eq '+') {
+ for (my $i=0;$i<@exon_starts;$i++) { # for each exon start
+ my $exon_start = $exon_starts[$i] + 1;
+ my $exon_end = $exon_ends[$i];
+ my (@utr_start, at utr_end,$cds_start,$cds_end);
+
+ if ($exon_start < $cdsStart) { # in a 5' UTR
+ push (@utr_start, $exon_start);
+ } elsif ($exon_start > $cdsEnd) {
+ push (@utr_start, $exon_start);
+ } else {
+ $cds_start = $exon_start;
+ }
+
+ if ($exon_end < $cdsStart) {
+ push (@utr_end, $exon_end);
+ } elsif ($exon_end > $cdsEnd) {
+ push (@utr_end, $exon_end);
+ } else {
+ $cds_end = $exon_end;
+ }
+
+ if ($utr_start[0] && !$utr_end[0]) { # half in half out on 5' end
+ $utr_end[0]= $cdsStart - 1;
+ $cds_start = $cdsStart;
+ $cds_end = $exon_end;
+ }
+
+ if ($utr_end[0] && !$utr_start[0]) { # half in half out on 3' end
+ $utr_start[0]= $cdsEnd + 1;
+ $cds_end = $cdsEnd;
+ $cds_start = $exon_start;
+ }
+
+ # If the CDS is within the exon
+ if (defined $utr_start[0] == defined $utr_end[0] &&
+ $utr_start[0] < $cdsStart && $utr_end[0] > $cdsEnd) {
+ $utr_end[0]= $cdsStart - 1;
+ $cds_start = $cdsStart;
+ $cds_end = $cdsEnd;
+
+ push (@utr_start, $cdsEnd + 1);
+ push (@utr_end, $exon_end);
+ }
+
+
+ die "programmer error, not an even number of utr_starts and
+utr_ends"
+ unless $#utr_start == $#utr_end;
+ die "programmer error, cds_start and no cds_end"
+ unless defined $cds_start == defined $cds_end;
+
+ for (my $i=0;$i<@utr_start;$i++) { # for each utr start
+ if (defined $utr_start[$i] && $utr_start[$i] <= $utr_end[$i] &&
+$utr_start[$i] < $cdsStart) {
+ print join
+("\t",$chrom,$SRC,"five_prime_UTR",$utr_start[$i],$utr_end[$i],'.',$strand,'.',"Parent=$id"),"\n"
+ } # end of if
+ } # end of foreach
+
+ if (defined $cds_start && $cds_start <= $cds_end) {
+ print join
+("\t",$chrom,$SRC,'CDS',$cds_start,$cds_end,'.',$strand,$phase,"Parent=$id"),"\n";
+ $phase = (($cds_end-$cds_start+1-$phase)) % 3;
+ }
+
+ for (my $i=0;$i<@utr_start;$i++) { # for each utr start
+ if (defined $utr_start[$i] && $utr_start[$i] <= $utr_end[$i] &&
+$utr_start[$i] > $cdsEnd) {
+ print join ("\t",$chrom,$SRC,"three_prime_UTR",,$utr_start[$i],
+$utr_end[$i],'.',$strand,'.',"Parent=$id"),"\n"
+ }
+ }
+ } # end of for each exon
+ } # matches if strand = +
+
+
+ if ($strand eq '-') {
+ my @lines;
+ for (my $i=@exon_starts-1; $i>=0; $i--) { # count backwards
+ my $exon_start = $exon_starts[$i] + 1;
+ my $exon_end = $exon_ends[$i];
+ my (@utr_start, at utr_end,$cds_start,$cds_end);
+
+ if ($exon_end > $cdsEnd) { # in a 5' UTR
+ push (@utr_end, $exon_end);
+ } elsif ($exon_end < $cdsStart) {
+ push (@utr_end, $exon_end);
+ } else {
+ $cds_end = $exon_end;
+ }
+
+ if ($exon_start > $cdsEnd) {
+ push (@utr_start, $exon_start);
+ } elsif ($exon_start < $cdsStart) {
+ push (@utr_start, $exon_start);
+ } else {
+ $cds_start = $exon_start;
+ }
+
+ if ($utr_start[0] && !$utr_end[0]) { # half in half out on 3' end
+ $utr_end[0] = $cdsStart - 1;
+ $cds_start = $cdsStart;
+ $cds_end = $exon_end;
+ }
+
+ if ($utr_end[0] && !$utr_start[0]) { # half in half out on 5' end
+ $utr_start[0] = $cdsEnd + 1;
+ $cds_end = $cdsEnd;
+ $cds_start = $exon_start;
+ }
+
+ # If the CDS is within the exon
+ if (defined $utr_start[0] == defined $utr_end[0] &&
+ $utr_start[0] < $cdsStart && $utr_end[0] > $cdsEnd) {
+ $utr_end[0]= $cdsStart - 1;
+ $cds_start = $cdsStart;
+ $cds_end = $cdsEnd;
+
+ push (@utr_start, $cdsEnd + 1);
+ push (@utr_end, $exon_end);
+ }
+
+ die "programmer error, not an even number of utr_starts and
+utr_ends"
+ unless $#utr_start == $#utr_end;
+
+ die "programmer error, cds_start and no cds_end" unless defined
+$cds_start == defined $cds_end;
+
+ for (my $i=0;$i<@utr_start;$i++) { # for each utr start
+ if (defined $utr_start[$i] && $utr_start[$i] <= $utr_end[$i] &&
+$utr_start[$i] > $cdsEnd) {
+ unshift @lines,join
+("\t",$chrom,$SRC,"five_prime_UTR",,$utr_start[$i],$utr_end[$i],'.',$strand,'.',"Parent=$id"),"\n"
+ }
+ } # end of for
+
+ if (defined $cds_start && $cds_start <= $cds_end) {
+ unshift @lines,join
+("\t",$chrom,$SRC,'CDS',$cds_start,$cds_end,'.',$strand,$phase,"Parent=$id"),"\n";
+ $phase = (($cds_end-$cds_start+1-$phase)) % 3;
+ }
+
+ for (my $i=0;$i<@utr_start;$i++) { # for each utr start
+ if (defined $utr_start[$i] && $utr_start[$i] <= $utr_end[$i] &&
+$utr_end[$i] < $cdsStart) {
+ unshift @lines,join
+("\t",$chrom,$SRC,"three_prime_UTR",$utr_start[$i],$utr_end[$i],'.',$strand,'.',"Parent=$id"),"\n"
+ }
+ } # end for
+ }
+ print @lines;
+ }
+} # end while <>
+
+__END__
+
+=head1 NAME
+
+ucsc_genes2gff.pl - Convert UCSC Genome Browser-format gene files into GFF
+files suitable for loading into gbrowse
+
+=head1 SYNOPSIS
+
+ % uscsc_genes2gff.pl [options] ucsc_file1 ucsc_file2...
+
+Options:
+
+ -src <string> Choose a source for the gene, default "UCSC"
+ -origin <integer> Choose a relative position to number from, default
+is "1"
+
+=head1 DESCRIPTION
+
+This script massages the gene files available from the "tables" link
+of the UCSC genome browser (genome.ucsc.edu) into a form suitable for
+loading of gbrowse. Warning: it only works with the gene tables.
+Other tables, such as EST alignments, contours and repeats, have their
+own formats which will require other scripts to parse.
+
+To use this script, get one or more UCSC tables, either from the
+"Tables" link on the browser, or from the UCSC Genome Browser FTP
+site. Give the table file as the argument to this script. You may
+want to provide an alternative "source" field. Otherwise this script
+defaults to "UCSC".
+
+ % pucsc_genes2gff.pl -src RefSeq refseq_data.ucsc > refseq.gff
+
+The resulting GFF file can then be loaded into a Bio::DB::GFF database
+using the following command:
+
+ % bulk_load_gff.pl -d <databasename> refseq.gff
+
+=head1 SEE ALSO
+
+L<Bio::DB::GFF>, L<bulk_load_gff.pl>, L<load_gff.pl>
+
+=head1 AUTHOR
+
+Lincoln Stein <lstein at cshl.org>.
+
+Copyright (c) 2003 Cold Spring Harbor Laboratory
+
+This library is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself. See DISCLAIMER.txt for
+disclaimers of warranty.
+
+=cut
+
Added: trunk/packages/gbrowse/trunk/conf/MobyServices/GbrowseServices.pm
===================================================================
--- trunk/packages/gbrowse/trunk/conf/MobyServices/GbrowseServices.pm (rev 0)
+++ trunk/packages/gbrowse/trunk/conf/MobyServices/GbrowseServices.pm 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,466 @@
+#!/usr/bin/perl -w
+package MobyServices::GbrowseServices;
+
+###################################################################
+# Non-modperl users should change this variable if needed to point
+# to the directory in which the configuration files are stored.
+#
+$CONF_DIR = '/home/charles/src/gbrowse-1.68/debian/gbrowse/etc//gbrowse.conf';
+#
+###################################################################
+
+
+
+
+
+
+
+#====================================================================
+#$Id: GbrowseServices.PMS,v 1.2 2004/01/07 22:21:49 markwilkinson Exp $
+
+use strict;
+use Text::Shellwords;
+use Bio::DB::GFF;
+use SOAP::Lite;
+use MOBY::CommonSubs qw{:all};
+use Bio::Graphics::Browser;
+use Bio::Graphics::Browser::Util;
+use vars qw(%dbh $CONFIG $authURI $CONF_DIR);
+
+sub _settings {
+ $CONF_DIR = conf_dir($CONF_DIR); # conf_dir() is exported from Util.pm
+
+ ## CONFIGURATION & INITIALIZATION ################################
+ # preliminaries -- read and/or refresh the configuration directory
+ $CONFIG = open_config($CONF_DIR); # open_config() is exported from Util.pm
+ my @sources = $CONFIG->sources; # get all data sources
+
+ foreach (@sources){ # grab the database handle for each source
+ $CONFIG->source($_);
+ my $db = open_database($CONFIG);
+ $dbh{$_}=$db;
+ }
+
+ open (IN, "$CONF_DIR/MobyServices/moby.conf") || die "\n**** GbrowseServices.pm couldn't open configuration file $CONF_DIR/MobyServices/moby.conf: $!\n";
+ while (<IN>){
+ chomp; next unless $_; # filter out blank lines
+ next if m/^#/; # filter out comment lines
+ last if $_ =~ /\[Namespace_Class_Mappings\]/;
+ my @res = shellwords($_); # parse the tokens key = value1 value2 value3
+ $CONFIG->{MOBY}->{$res[0]} = [@res[2..scalar(@res)]]; # add them to the existing config with a new tag MOBY in key = \@values format
+ }
+ while (<IN>){ # now process the namespace mappings
+ chomp; next unless $_; # filter out blank lines
+ next if m/^#/; # filter out comment lines
+ my @res = shellwords($_); # parse the tokens key = value1 value2 value3
+ $CONFIG->{'MOBY'}->{'NAMESPACE'}->{$res[0]} = [$res[2]]; # add them to the existing config with a new tag MOBY in key = \@values format
+ }
+}
+
+sub _doValidationStuff {
+ my $authURI = $CONFIG->{'MOBY'}->{'authURI'};
+ $authURI = shift(@$authURI); $authURI ||='unknown.org';
+
+ my $reference = $CONFIG->{'MOBY'}->{'Reference'};
+ $reference = shift(@$reference); $reference ||='';
+ unless ($reference){
+ print STDERR "\n\nMobyServices::GbrowseServices - you have not set a reference class in your moby.conf file\n\n";
+ return SOAP::Data->type('base64' => responseHeader($authURI) . responseFooter());
+ }
+
+ my (@feat_namespaces) = keys %{$CONFIG->{MOBY}->{NAMESPACE}};
+ my @validNS = validateNamespaces($reference, at feat_namespaces); # ONLY do this if you are intending to be namespace aware!
+ unless (scalar(@validNS)){
+ print STDERR "\n\nMobyServices::GbrowseServices - namespace $reference does not exist in the MOBY Namespace ontology\n\n";
+ return SOAP::Data->type('base64' => responseHeader($authURI) . responseFooter());
+ }
+
+ return ($authURI, \@validNS);
+}
+
+sub GbrowseGetFeatureGFF2 {
+ my ($caller, $data) = @_;
+ _settings();
+ my ($authURI, $validNSs) = _doValidationStuff();
+
+ my $MOBY_RESPONSE = "";
+ foreach my $source($CONFIG->sources){
+ $CONFIG->source($source); # set the current source
+ next unless (my $db = $dbh{$source}); # get the database object
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ next unless (scalar(@inputs));
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input)){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ $namespace ||="";
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless validateThisNamespace($namespace, @{$validNSs});
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ # okay, we need to map the MOBY namespace back into our namespace system
+ my $Groupname = $CONFIG->{MOBY}->{NAMESPACE}->{$namespace};
+ unless ($Groupname){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ print STDERR "** MOBY Services error - Trying to map apparently valid namespace: '$namespace' but not found\n";
+ next;
+ }
+ my @features = $db->get_feature_by_name(-class => $Groupname, -name => $identifier);
+ my $gff = "";
+ foreach my $feat(@features){
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $feat;
+ $gff .= $feat->gff_string."\n";
+ foreach my $sub($feat->sub_SeqFeature){
+ next unless $sub;
+ $gff .= $sub->gff_string."\n";
+ }
+ }
+ $MOBY_RESPONSE .= simpleResponse("<moby:GFF2 moby:namespace='$namespace' moby:id='$identifier'>\n$gff\n</moby:GFF2>", "", $qID);
+ }
+ }
+ }
+ #print STDERR (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter));
+}
+
+sub GbrowseGetFeatureGFF3 {
+ my ($caller, $data) = @_;
+ _settings();
+ my ($authURI, $validNSs) = _doValidationStuff();
+
+ my $MOBY_RESPONSE = "";
+ foreach my $source($CONFIG->sources){
+ $CONFIG->source($source); # set the current source
+ next unless (my $db = $dbh{$source}); # get the database object
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ next unless (scalar(@inputs));
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input)){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ $namespace ||="";
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless validateThisNamespace($namespace, @{$validNSs});
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ # okay, we need to map the MOBY namespace back into our namespace system
+ my $Groupname = $CONFIG->{MOBY}->{NAMESPACE}->{$namespace};
+ unless ($Groupname){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ print STDERR "** MOBY Services error - Trying to map apparently valid namespace: '$namespace' but not found\n";
+ next;
+ }
+ my @features = $db->get_feature_by_name(-class => $Groupname, -name => $identifier);
+ my $gff = "";
+ foreach my $feat(@features){
+ $feat->version(3); # set to GFF3
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $feat;
+ $gff .= $feat->gff_string."\n";
+ foreach my $sub($feat->sub_SeqFeature){
+ next unless $sub;
+ $sub->version(3);
+ $gff .= $sub->gff_string."\n";
+ }
+ }
+ $MOBY_RESPONSE .= simpleResponse("<moby:GFF2 moby:namespace='$namespace' moby:id='$identifier'>\n$gff\n</moby:GFF2>", "", $qID);
+ }
+ }
+ }
+ #print STDERR (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter));
+}
+
+sub GbrowseGetFeatureSequenceObject {
+ my ($caller, $data) = @_;
+ _settings();
+ my ($authURI, $validNSs) = _doValidationStuff();
+ my %types = ('dna', 'DNASequence', 'rna', 'RNASequence', 'protein', 'AminoAcidSequence');
+
+ my $MOBY_RESPONSE = "";
+ foreach my $source($CONFIG->sources){
+ $CONFIG->source($source); # set the current source
+ next unless (my $db = $dbh{$source}); # get the database object
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ next unless (scalar(@inputs));
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input)){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ; # send empty response for empty input
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input); # get the namespace
+ $namespace ||="";
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless validateThisNamespace($namespace, @{$validNSs}); #invalid namespace treated as empty query
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ # okay, we need to map the MOBY namespace back into our namespace system
+ my $Groupname = $CONFIG->{MOBY}->{NAMESPACE}->{$namespace}; # map the namespace to our database group name
+ unless ($Groupname){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ; # if it is invlid, send empty respnse and tell the maintainer that something is goofy!
+ print STDERR "** MOBY Services error - Trying to map apparently valid namespace: '$namespace' but not found\n";
+ next;
+ }
+ my @features = $db->get_feature_by_name(-class => $Groupname, -name => $identifier); # get feature from DB
+ my $gff = "";
+ foreach my $feat(@features){
+ $feat->version(3); # set to GFF3
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $feat;
+
+ my $seq = $feat->seq;
+ $seq =~ s/\s//g;
+ my $length = $feat->length;
+ my $objtype = $types{$feat->alphabet};
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $objtype;
+ $MOBY_RESPONSE .= simpleResponse("<moby:$objtype moby:namespace='$namespace' moby:id='$identifier'>
+ <moby:String namespace='' id=''>$seq</moby:String>
+ <moby:Integer namespace='' id=''>$length</moby:Integer>
+ </moby:$objtype>", "", $qID);
+ }
+ }
+ }
+ }
+ #print STDERR (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter));
+}
+
+sub GbrowseGetReferenceGFF2 { # DO THIS ONE!!
+ my ($caller, $data) = @_;
+ _settings();
+ my ($authURI, $validNSs) = _doValidationStuff();
+
+ my $MOBY_RESPONSE = "";
+ foreach my $source($CONFIG->sources){
+ $CONFIG->source($source); # set the current source
+ next unless (my $db = $dbh{$source}); # get the database object
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ next unless (scalar(@inputs));
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input)){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless validateThisNamespace($namespace, @{$validNSs});
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ my $seg = $db->segment(-name => $identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $seg;
+ my $gff = join "\n", map {$_->gff_string} ($seg->get_SeqFeatures);
+ $MOBY_RESPONSE .= simpleResponse("<moby:GFF2 moby:namespace='$namespace' moby:id='$identifier'>\n$gff\n</moby:GFF2>", "", $qID);
+ }
+ }
+ }
+ #print STDERR (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter));
+}
+
+sub GbrowseGetReferenceDNASequenceWithFeatures {
+ my ($caller, $data) = @_;
+ _settings();
+ my ($authURI, $validNSs) = _doValidationStuff();
+
+ my $MOBY_RESPONSE = "";
+ foreach my $source($CONFIG->sources){
+ $CONFIG->source($source); # set the current source
+ next unless (my $db = $dbh{$source}); # get the database object
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ next unless (scalar(@inputs));
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input)){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless validateThisNamespace($namespace, @{$validNSs});
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ my $seg = $db->segment(-name => $identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $seg;
+ my $seq = $seg->seq; $seq =~ s/\S//g;
+ my $length = $seg->length; # DNASequenceWithGFFFeatures
+ my $mobyresp = "<moby:DNASequenceWithGFFFeatures moby:namespace='$namespace' moby:id='$identifier'>
+ <moby:String moby:namespace='' moby:id=''>$seq</moby:String>
+ <moby:Integer moby:namespace='' moby:id=''>$length</moby:Integer>
+ ";
+ foreach my $feat($seg->get_SeqFeatures){$mobyresp .="
+ <moby:BasicGFFSequenceFeature namespace='' id=''>
+ <String namespace='' id='' articleName='reference'></String>
+ <String namespace='' id='' articleName='source'></String>
+ <String namespace='' id='' articleName='method'></String>
+ <Integer namespace='' id='' articleName='start'></Integer>
+ <Integer namespace='' id='' articleName='stop'></Integer>
+ <Float namespace='' id='' articleName='score'></Float>
+ <String namespace='' id='' articleName='strand'></String>
+ <String namespace='' id='' articleName='frame'></String>
+ <String namespace='' id='' articleName='phase'></String>"
+
+ }
+ my $gff = join "\n", map {$_->gff_string} ($seg->get_SeqFeatures);
+ $MOBY_RESPONSE .= simpleResponse("<moby:GFF2 moby:namespace='$namespace' moby:id='$identifier'>\n$gff\n</moby:GFF2>", "", $qID);
+ }
+ }
+ }
+ #print STDERR (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter));
+}
+
+sub GbrowseGetReferenceGFF3 {
+ my ($caller, $data) = @_;
+ _settings();
+ my ($authURI, $validNSs) = _doValidationStuff();
+
+ my $MOBY_RESPONSE = "";
+ foreach my $source($CONFIG->sources){
+ $CONFIG->source($source); # set the current source
+ next unless (my $db = $dbh{$source}); # get the database object
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ next unless (scalar(@inputs));
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input)){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless validateThisNamespace($namespace, @{$validNSs});
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ my $seg = $db->segment(-name => $identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $seg;
+ my $gff = join "\n", map {$_->version(3); $_->gff_string} ($seg->get_SeqFeatures);
+ my $seq = $seg->seq;
+ $seq =~ s/\s//g;
+ $seq =~ s/(\S{70})/$1\n/g;
+ my $fasta = ">$identifier\n$seq\n";
+ $MOBY_RESPONSE .= simpleResponse("<moby:GFF3 moby:namespace='$namespace' moby:id='$identifier'>\n$gff\n###FASTA\n$fasta\n</moby:GFF3>", "", $qID);
+ }
+ }
+ }
+ #print STDERR (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter));
+}
+
+
+sub GbrowseGetReferenceFasta {
+ my ($caller, $data) = @_;
+ _settings();
+ my ($authURI, $validNSs) = _doValidationStuff();
+
+ my $MOBY_RESPONSE;
+ foreach my $source($CONFIG->sources){
+ $CONFIG->source($source); # set the current source
+ next unless (my $db = $dbh{$source}); # get the database object
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ next unless (scalar(@inputs));
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input)){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless validateThisNamespace($namespace, @{$validNSs});
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ my $seg = $db->segment(-name => $identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $seg;
+ my $seq = $seg->seq;
+ $seq =~ s/\s//g;
+ $seq =~ s/(\S{70})/$1\n/g;
+ my $fasta = ">$identifier\n$seq\n";
+ $MOBY_RESPONSE .= simpleResponse("<moby:FASTA moby:namespace='$namespace' moby:id='$identifier'>\n$fasta\n</moby:FASTA>", "", $qID);
+ }
+ }
+ }
+ #print STDERR (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter));
+}
+
+
+sub GbrowseGetReferenceSeqObj {
+ my ($caller, $data) = @_;
+ _settings();
+ my ($authURI, $validNSs) = _doValidationStuff();
+ my %types = ('dna', 'DNASequence', 'rna', 'RNASequence', 'protein', 'AminoAcidSequence');
+
+ my $MOBY_RESPONSE = "";
+ foreach my $source($CONFIG->sources){
+ $CONFIG->source($source); # set the current source
+ next unless (my $db = $dbh{$source}); # get the database object
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ next unless (scalar(@inputs));
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input)){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless validateThisNamespace($namespace, @{$validNSs});
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ my $seg = $db->segment(-name => $identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $seg;
+ my $seq = $seg->seq;
+ $seq =~ s/\s//g;
+ my $length = $seg->length;
+ my $objtype = $types{$seg->alphabet};
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $objtype;
+ $MOBY_RESPONSE .= simpleResponse("<moby:$objtype moby:namespace='$namespace' moby:id='$identifier'>
+ <moby:String namespace='' id=''>$seq</moby:String>
+ <moby:Integer namespace='' id=''>$length</moby:Integer>
+ </moby:$objtype>", "", $qID);
+ }
+ }
+ }
+ #print STDERR (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter));
+}
+
+
+sub GbrowseGetSomeFeatureSequence {
+ my ($caller, $data) = @_;
+ _settings();
+ my ($authURI, $validNSs) = _doValidationStuff();
+ my %types = ('dna', 'DNASequence', 'rna', 'RNASequence', 'protein', 'AminoAcidSequence');
+
+ my $MOBY_RESPONSE = "";
+ foreach my $source($CONFIG->sources){
+ $CONFIG->source($source); # set the current source
+ next unless (my $db = $dbh{$source}); # get the database object
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ next unless (scalar(@inputs));
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input)){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless validateThisNamespace($namespace, @{$validNSs});
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ my $seg = $db->segment(-name => $identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $seg;
+ my $seq = $seg->seq;
+ $seq =~ s/\s//g;
+ my $length = $seg->length;
+ my $objtype = $types{$seg->alphabet};
+ (($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $objtype;
+ $MOBY_RESPONSE .= simpleResponse("<moby:$objtype moby:namespace='$namespace' moby:id='$identifier'>
+ <moby:String namespace='' id=''>$seq</moby:String>
+ <moby:Integer namespace='' id=''>$length</moby:Integer>
+ </moby:$objtype>", "", $qID);
+ }
+ }
+ }
+ #print STDERR (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader($authURI) . $MOBY_RESPONSE . responseFooter));
+}
+
+
+1;
+
+#===========================================
+
+
+
Property changes on: trunk/packages/gbrowse/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/gbrowse/trunk/debian/README.Debian
===================================================================
--- trunk/packages/gbrowse/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/README.Debian 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,6 @@
+GBrowse for Debian
+---------------------------------
+
+<possible notes regarding this package - if none, delete this file>
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 13 Jun 2007 19:07:01 +0900
Added: trunk/packages/gbrowse/trunk/debian/changelog
===================================================================
--- trunk/packages/gbrowse/trunk/debian/changelog (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/changelog 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,6 @@
+gbrowse (1.68-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 13 Jun 2007 19:07:01 +0900
+
Added: trunk/packages/gbrowse/trunk/debian/compat
===================================================================
--- trunk/packages/gbrowse/trunk/debian/compat (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/compat 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1 @@
+5
Added: trunk/packages/gbrowse/trunk/debian/control
===================================================================
--- trunk/packages/gbrowse/trunk/debian/control (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/control 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,30 @@
+Source: gbrowse
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>
+Build-Depends: debhelper (>= 5), bioperl (>= 1.5.2), quilt
+Standards-Version: 3.7.2
+
+Package: gbrowse
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: The Generic Genome Browser from GMOD
+ The Generic Genome Browser is a combination of database and interactive Web
+ page for manipulating and displaying annotations on genomes. Some of its
+ features:
+ * Simultaneous bird's eye and detailed views of the genome.
+ * Scroll, zoom, center.
+ * Attach arbitrary URLs to any annotation.
+ * Order and appearance of tracks are customizable by administrator and end-user.
+ * Search by annotation ID, name, or comment.
+ * Supports third party annotation using GFF formats.
+ * Settings persist across sessions.
+ * DNA and GFF dumps.
+ * Connectivity to different databases, including BioSQL and Chado.
+ * Multi-language support.
+ * Third-party feature loading.
+ * Customizable plug-in architecture (e.g. run BLAST, dump & import many formats,
+ find oligonucleotides, design primers, create restriction maps, edit features)
+ .
+ Homepage: http://www.gmod.org/wiki/index.php/GBrowse
Added: trunk/packages/gbrowse/trunk/debian/copyright
===================================================================
--- trunk/packages/gbrowse/trunk/debian/copyright (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/copyright 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,29 @@
+This package was debianized by Charles Plessy <charles-debian-nospam at plessy.org> on
+Wed, 13 Jun 2007 19:07:01 +0900.
+
+It was downloaded from <fill in http/ftp site>
+
+Upstream Author: <put author(s) name and email here>
+
+Copyright: <put the year(s) of the copyright, and the names of the
+ copyright holder(s) here>
+
+License:
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the "Artistic License" which comes with Debian.
+
+ THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
+ WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
+ OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+
+On Debian systems, the complete text of the Artistic License
+can be found in `/usr/share/common-licenses/Artistic'.
+
+The Debian packaging is (C) 2007, Charles Plessy <charles-debian-nospam at plessy.org> and
+is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
+
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
+
Added: trunk/packages/gbrowse/trunk/debian/dirs
===================================================================
--- trunk/packages/gbrowse/trunk/debian/dirs (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/dirs 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,2 @@
+usr/bin
+usr/sbin
Added: trunk/packages/gbrowse/trunk/debian/docs
===================================================================
--- trunk/packages/gbrowse/trunk/debian/docs (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/docs 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,4 @@
+README
+README.gff3
+README.sessions
+TODO
Added: trunk/packages/gbrowse/trunk/debian/generic-genome-browser.doc-base.EX
===================================================================
--- trunk/packages/gbrowse/trunk/debian/generic-genome-browser.doc-base.EX (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/generic-genome-browser.doc-base.EX 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,22 @@
+Document: generic-genome-browser
+Title: Debian generic-genome-browser Manual
+Author: <insert document author here>
+Abstract: This manual describes what generic-genome-browser is
+ and how it can be used to
+ manage online manuals on Debian systems.
+Section: unknown
+
+Format: debiandoc-sgml
+Files: /usr/share/doc/generic-genome-browser/generic-genome-browser.sgml.gz
+
+Format: postscript
+Files: /usr/share/doc/generic-genome-browser/generic-genome-browser.ps.gz
+
+Format: text
+Files: /usr/share/doc/generic-genome-browser/generic-genome-browser.text.gz
+
+Format: HTML
+Index: /usr/share/doc/generic-genome-browser/html/index.html
+Files: /usr/share/doc/generic-genome-browser/html/*.html
+
+
Added: trunk/packages/gbrowse/trunk/debian/patches/10_usrlocalperl.patch
===================================================================
--- trunk/packages/gbrowse/trunk/debian/patches/10_usrlocalperl.patch (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/patches/10_usrlocalperl.patch 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,10 @@
+Index: gbrowse-1.68/contrib/blast2gff.pl
+===================================================================
+--- gbrowse-1.68.orig/contrib/blast2gff.pl 2007-06-14 22:47:19.000000000 +0900
++++ gbrowse-1.68/contrib/blast2gff.pl 2007-06-14 22:47:37.000000000 +0900
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ =head1 NAME
+
Added: trunk/packages/gbrowse/trunk/debian/patches/series
===================================================================
--- trunk/packages/gbrowse/trunk/debian/patches/series (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/patches/series 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1 @@
+10_usrlocalperl.patch
Added: trunk/packages/gbrowse/trunk/debian/rules
===================================================================
--- trunk/packages/gbrowse/trunk/debian/rules (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/rules 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,76 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+include /usr/share/quilt/quilt.make
+
+configure: configure-stamp
+configure-stamp:
+ dh_testdir
+ perl Makefile.PL \
+ DESTDIR=$(CURDIR)/debian/gbrowse \
+ CGIBIN=$(CURDIR)/debian/gbrowse/usr/lib/cgi-bin \
+ CONF=$(CURDIR)/debian/gbrowse/etc/ \
+ HTDOCS=$(CURDIR)/debian/gbrowse/var/www \
+ INSTALLDIRS=vendor \
+ VENDORARCHEXP=/usr/share/perl5
+ touch configure-stamp
+
+build: patch build-stamp
+build-stamp: configure-stamp
+ dh_testdir
+ $(MAKE) OPTIMIZE="-O2 -g -Wall"
+ touch $@
+
+clean: unpatch configure-stamp
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp
+ $(MAKE) clean
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+ # Add here commands to install the package into debian/generic-genome-browser.
+ $(MAKE) DESTDIR=$(CURDIR)/debian/gbrowse install
+
+ # UGLY WORKAROUND TO A CONFLICT WITH BIOPERL 1.5.2
+ rm $(CURDIR)/debian/gbrowse/usr/share/man/man3/Bio::Graphics::FeatureFile.3pm
+
+binary-indep: build install
+
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs Changes
+ dh_installdocs
+ dh_installexamples
+# dh_install
+# dh_installmenu
+# dh_installdebconf
+# dh_installlogrotate
+# dh_installemacsen
+# dh_installpam
+# dh_installmime
+# dh_python
+# dh_installinit
+# dh_installcron
+# dh_installinfo
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+# dh_perl
+# dh_makeshlibs
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure
Property changes on: trunk/packages/gbrowse/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/gbrowse/trunk/debian/watch.ex
===================================================================
--- trunk/packages/gbrowse/trunk/debian/watch.ex (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/watch.ex 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,22 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+
+# Uncomment to examine a Webpage
+# <Webpage URL> <string match>
+#http://www.example.com/downloads.php generic-genome-browser-(.*)\.tar\.gz
+
+# Uncomment to examine a Webserver directory
+#http://www.example.com/pub/generic-genome-browser-(.*)\.tar\.gz
+
+# Uncommment to examine a FTP server
+#ftp://ftp.example.com/pub/generic-genome-browser-(.*)\.tar\.gz debian uupdate
+
+# Uncomment to find new files on sourceforge, for debscripts >= 2.9
+# http://sf.net/generic-genome-browser/generic-genome-browser-(.*)\.tar\.gz
+
+
Added: trunk/packages/gbrowse/trunk/libalign/Makefile.old
===================================================================
--- trunk/packages/gbrowse/trunk/libalign/Makefile.old (rev 0)
+++ trunk/packages/gbrowse/trunk/libalign/Makefile.old 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,737 @@
+# This Makefile is for the Bio::Graphics::Browser::CAlign extension to perl.
+#
+# It was generated automatically by MakeMaker version
+# 6.30_01 (Revision: Revision: 4535 ) from the contents of
+# Makefile.PL. Don't edit this file, edit Makefile.PL instead.
+#
+# ANY CHANGES MADE HERE WILL BE LOST!
+#
+# MakeMaker ARGV: (q[DESTDIR=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse], q[INSTALLDIRS=vendor], q[VENDORARCHEXP=/usr/share/perl5])
+#
+# MakeMaker Parameters:
+
+# ABSTRACT_FROM => q[CAlign.pm]
+# AUTHOR => q[A. U. Thor <a.u.thor at a.galaxy.far.far.away>]
+# DEFINE => q[]
+# INC => q[]
+# LIBS => [q[]]
+# NAME => q[Bio::Graphics::Browser::CAlign]
+# PREREQ_PM => { }
+# VERSION_FROM => q[CAlign.pm]
+
+# --- MakeMaker post_initialize section:
+
+
+# --- MakeMaker const_config section:
+
+# These definitions are from config.sh (via /usr/lib/perl/5.8/Config.pm)
+
+# They may have been overridden via Makefile.PL or on the command line
+AR = ar
+CC = cc
+CCCDLFLAGS = -fPIC
+CCDLFLAGS = -Wl,-E
+DLEXT = so
+DLSRC = dl_dlopen.xs
+LD = cc
+LDDLFLAGS = -shared -L/usr/local/lib
+LDFLAGS = -L/usr/local/lib
+LIBC = /lib/libc-2.3.6.so
+LIB_EXT = .a
+OBJ_EXT = .o
+OSNAME = linux
+OSVERS = 2.6.8-powerpc-smp
+RANLIB = :
+SITELIBEXP = /usr/local/share/perl/5.8.8
+SITEARCHEXP = /usr/local/lib/perl/5.8.8
+SO = so
+EXE_EXT =
+FULL_AR = /usr/bin/ar
+VENDORARCHEXP = /usr/lib/perl5
+VENDORLIBEXP = /usr/share/perl5
+
+
+# --- MakeMaker constants section:
+AR_STATIC_ARGS = cr
+DIRFILESEP = /
+DFSEP = $(DIRFILESEP)
+NAME = Bio::Graphics::Browser::CAlign
+NAME_SYM = Bio_Graphics_Browser_CAlign
+VERSION = 1.00
+VERSION_MACRO = VERSION
+VERSION_SYM = 1_00
+DEFINE_VERSION = -D$(VERSION_MACRO)=\"$(VERSION)\"
+XS_VERSION = 1.00
+XS_VERSION_MACRO = XS_VERSION
+XS_DEFINE_VERSION = -D$(XS_VERSION_MACRO)=\"$(XS_VERSION)\"
+INST_ARCHLIB = ../blib/arch
+INST_SCRIPT = ../blib/script
+INST_BIN = ../blib/bin
+INST_LIB = ../blib/lib
+INST_MAN1DIR = ../blib/man1
+INST_MAN3DIR = ../blib/man3
+MAN1EXT = 1p
+MAN3EXT = 3pm
+INSTALLDIRS = site
+DESTDIR =
+PREFIX = /usr
+PERLPREFIX = $(PREFIX)
+SITEPREFIX = $(PREFIX)/local
+VENDORPREFIX = $(PREFIX)
+INSTALLPRIVLIB = $(PERLPREFIX)/share/perl/5.8
+DESTINSTALLPRIVLIB = $(DESTDIR)$(INSTALLPRIVLIB)
+INSTALLSITELIB = $(SITEPREFIX)/share/perl/5.8.8
+DESTINSTALLSITELIB = $(DESTDIR)$(INSTALLSITELIB)
+INSTALLVENDORLIB = $(VENDORPREFIX)/share/perl5
+DESTINSTALLVENDORLIB = $(DESTDIR)$(INSTALLVENDORLIB)
+INSTALLARCHLIB = $(PERLPREFIX)/lib/perl/5.8
+DESTINSTALLARCHLIB = $(DESTDIR)$(INSTALLARCHLIB)
+INSTALLSITEARCH = $(SITEPREFIX)/lib/perl/5.8.8
+DESTINSTALLSITEARCH = $(DESTDIR)$(INSTALLSITEARCH)
+INSTALLVENDORARCH = $(VENDORPREFIX)/lib/perl5
+DESTINSTALLVENDORARCH = $(DESTDIR)$(INSTALLVENDORARCH)
+INSTALLBIN = $(PERLPREFIX)/bin
+DESTINSTALLBIN = $(DESTDIR)$(INSTALLBIN)
+INSTALLSITEBIN = $(SITEPREFIX)/bin
+DESTINSTALLSITEBIN = $(DESTDIR)$(INSTALLSITEBIN)
+INSTALLVENDORBIN = $(VENDORPREFIX)/bin
+DESTINSTALLVENDORBIN = $(DESTDIR)$(INSTALLVENDORBIN)
+INSTALLSCRIPT = $(PERLPREFIX)/bin
+DESTINSTALLSCRIPT = $(DESTDIR)$(INSTALLSCRIPT)
+INSTALLSITESCRIPT = $(SITEPREFIX)/bin
+DESTINSTALLSITESCRIPT = $(DESTDIR)$(INSTALLSITESCRIPT)
+INSTALLVENDORSCRIPT = $(VENDORPREFIX)/bin
+DESTINSTALLVENDORSCRIPT = $(DESTDIR)$(INSTALLVENDORSCRIPT)
+INSTALLMAN1DIR = $(PERLPREFIX)/share/man/man1
+DESTINSTALLMAN1DIR = $(DESTDIR)$(INSTALLMAN1DIR)
+INSTALLSITEMAN1DIR = $(SITEPREFIX)/man/man1
+DESTINSTALLSITEMAN1DIR = $(DESTDIR)$(INSTALLSITEMAN1DIR)
+INSTALLVENDORMAN1DIR = $(VENDORPREFIX)/share/man/man1
+DESTINSTALLVENDORMAN1DIR = $(DESTDIR)$(INSTALLVENDORMAN1DIR)
+INSTALLMAN3DIR = $(PERLPREFIX)/share/man/man3
+DESTINSTALLMAN3DIR = $(DESTDIR)$(INSTALLMAN3DIR)
+INSTALLSITEMAN3DIR = $(SITEPREFIX)/man/man3
+DESTINSTALLSITEMAN3DIR = $(DESTDIR)$(INSTALLSITEMAN3DIR)
+INSTALLVENDORMAN3DIR = $(VENDORPREFIX)/share/man/man3
+DESTINSTALLVENDORMAN3DIR = $(DESTDIR)$(INSTALLVENDORMAN3DIR)
+PERL_LIB = /usr/share/perl/5.8
+PERL_ARCHLIB = /usr/lib/perl/5.8
+LIBPERL_A = libperl.a
+FIRST_MAKEFILE = Makefile
+MAKEFILE_OLD = Makefile.old
+MAKE_APERL_FILE = Makefile.aperl
+PERLMAINCC = $(CC)
+PERL_INC = /usr/lib/perl/5.8/CORE
+PERL = /usr/bin/perl
+FULLPERL = /usr/bin/perl
+ABSPERL = $(PERL)
+PERLRUN = $(PERL)
+FULLPERLRUN = $(FULLPERL)
+ABSPERLRUN = $(ABSPERL)
+PERLRUNINST = $(PERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
+FULLPERLRUNINST = $(FULLPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
+ABSPERLRUNINST = $(ABSPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
+PERL_CORE = 0
+PERM_RW = 644
+PERM_RWX = 755
+
+MAKEMAKER = /usr/share/perl/5.8/ExtUtils/MakeMaker.pm
+MM_VERSION = 6.30_01
+MM_REVISION = Revision: 4535
+
+# FULLEXT = Pathname for extension directory (eg Foo/Bar/Oracle).
+# BASEEXT = Basename part of FULLEXT. May be just equal FULLEXT. (eg Oracle)
+# PARENT_NAME = NAME without BASEEXT and no trailing :: (eg Foo::Bar)
+# DLBASE = Basename part of dynamic library. May be just equal BASEEXT.
+FULLEXT = Bio/Graphics/Browser/CAlign
+BASEEXT = CAlign
+PARENT_NAME = Bio::Graphics::Browser
+DLBASE = $(BASEEXT)
+VERSION_FROM = CAlign.pm
+INC =
+DEFINE =
+OBJECT = $(BASEEXT)$(OBJ_EXT)
+LDFROM = $(OBJECT)
+LINKTYPE = dynamic
+BOOTDEP =
+
+# Handy lists of source code files:
+XS_FILES = CAlign.xs
+C_FILES = CAlign.c
+O_FILES = CAlign.o
+H_FILES = realign.h
+MAN1PODS =
+MAN3PODS = CAlign.pm
+
+# Where is the Config information that we are using/depend on
+CONFIGDEP = $(PERL_ARCHLIB)$(DFSEP)Config.pm $(PERL_INC)$(DFSEP)config.h
+
+# Where to build things
+INST_LIBDIR = $(INST_LIB)/Bio/Graphics/Browser
+INST_ARCHLIBDIR = $(INST_ARCHLIB)/Bio/Graphics/Browser
+
+INST_AUTODIR = $(INST_LIB)/auto/$(FULLEXT)
+INST_ARCHAUTODIR = $(INST_ARCHLIB)/auto/$(FULLEXT)
+
+INST_STATIC = $(INST_ARCHAUTODIR)/$(BASEEXT)$(LIB_EXT)
+INST_DYNAMIC = $(INST_ARCHAUTODIR)/$(DLBASE).$(DLEXT)
+INST_BOOT = $(INST_ARCHAUTODIR)/$(BASEEXT).bs
+
+# Extra linker info
+EXPORT_LIST =
+PERL_ARCHIVE =
+PERL_ARCHIVE_AFTER =
+
+
+TO_INST_PM = CAlign.pm
+
+PM_TO_BLIB = CAlign.pm \
+ $(INST_LIB)/Bio/Graphics/Browser/CAlign.pm
+
+
+# --- MakeMaker platform_constants section:
+MM_Unix_VERSION = 1.50_01
+PERL_MALLOC_DEF = -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc
+
+
+# --- MakeMaker tool_autosplit section:
+# Usage: $(AUTOSPLITFILE) FileToSplit AutoDirToSplitInto
+AUTOSPLITFILE = $(ABSPERLRUN) -e 'use AutoSplit; autosplit($$ARGV[0], $$ARGV[1], 0, 1, 1)'
+
+
+
+# --- MakeMaker tool_xsubpp section:
+
+XSUBPPDIR = /usr/share/perl/5.8.8/ExtUtils
+XSUBPP = $(XSUBPPDIR)$(DFSEP)xsubpp
+XSUBPPRUN = $(PERLRUN) $(XSUBPP)
+XSPROTOARG =
+XSUBPPDEPS = /usr/share/perl/5.8/ExtUtils/typemap $(XSUBPP)
+XSUBPPARGS = -typemap /usr/share/perl/5.8/ExtUtils/typemap
+XSUBPP_EXTRA_ARGS =
+
+
+# --- MakeMaker tools_other section:
+SHELL = /bin/sh
+CHMOD = chmod
+CP = cp
+MV = mv
+NOOP = $(SHELL) -c true
+NOECHO = @
+RM_F = rm -f
+RM_RF = rm -rf
+TEST_F = test -f
+TOUCH = touch
+UMASK_NULL = umask 0
+DEV_NULL = > /dev/null 2>&1
+MKPATH = $(ABSPERLRUN) "-MExtUtils::Command" -e mkpath
+EQUALIZE_TIMESTAMP = $(ABSPERLRUN) "-MExtUtils::Command" -e eqtime
+ECHO = echo
+ECHO_N = echo -n
+UNINST = 0
+VERBINST = 0
+MOD_INSTALL = $(ABSPERLRUN) -MExtUtils::Install -e 'install({@ARGV}, '\''$(VERBINST)'\'', 0, '\''$(UNINST)'\'');'
+DOC_INSTALL = $(ABSPERLRUN) "-MExtUtils::Command::MM" -e perllocal_install
+UNINSTALL = $(ABSPERLRUN) "-MExtUtils::Command::MM" -e uninstall
+WARN_IF_OLD_PACKLIST = $(ABSPERLRUN) "-MExtUtils::Command::MM" -e warn_if_old_packlist
+MACROSTART =
+MACROEND =
+USEMAKEFILE = -f
+FIXIN = $(PERLRUN) "-MExtUtils::MY" -e "MY->fixin(shift)"
+
+
+# --- MakeMaker makemakerdflt section:
+makemakerdflt: all
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker dist section skipped.
+
+# --- MakeMaker macro section:
+
+
+# --- MakeMaker depend section:
+
+
+# --- MakeMaker cflags section:
+
+CCFLAGS = -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBIAN -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
+OPTIMIZE = -O2
+PERLTYPE =
+MPOLLUTE =
+
+
+# --- MakeMaker const_loadlibs section:
+
+# Bio::Graphics::Browser::CAlign might depend on some other libraries:
+# See ExtUtils::Liblist for details
+#
+
+
+# --- MakeMaker const_cccmd section:
+CCCMD = $(CC) -c $(PASTHRU_INC) $(INC) \
+ $(CCFLAGS) $(OPTIMIZE) \
+ $(PERLTYPE) $(MPOLLUTE) $(DEFINE_VERSION) \
+ $(XS_DEFINE_VERSION)
+
+# --- MakeMaker post_constants section:
+
+
+# --- MakeMaker pasthru section:
+
+PASTHRU = LIBPERL_A="$(LIBPERL_A)"\
+ LINKTYPE="$(LINKTYPE)"\
+ OPTIMIZE="$(OPTIMIZE)"\
+ PREFIX="$(PREFIX)"\
+ PASTHRU_DEFINE="$(PASTHRU_DEFINE)"\
+ PASTHRU_INC="$(PASTHRU_INC)"
+
+
+# --- MakeMaker special_targets section:
+.SUFFIXES : .xs .c .C .cpp .i .s .cxx .cc $(OBJ_EXT)
+
+.PHONY: all config static dynamic test linkext manifest blibdirs clean realclean disttest distdir
+
+
+
+# --- MakeMaker c_o section:
+
+.c.i:
+ cc -E -c $(PASTHRU_INC) $(INC) \
+ $(CCFLAGS) $(OPTIMIZE) \
+ $(PERLTYPE) $(MPOLLUTE) $(DEFINE_VERSION) \
+ $(XS_DEFINE_VERSION) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c > $*.i
+
+.c.s:
+ $(CCCMD) -S $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c
+
+.c$(OBJ_EXT):
+ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c
+
+.C$(OBJ_EXT):
+ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.C
+
+.cpp$(OBJ_EXT):
+ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cpp
+
+.cxx$(OBJ_EXT):
+ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cxx
+
+.cc$(OBJ_EXT):
+ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cc
+
+
+# --- MakeMaker xs_c section:
+
+.xs.c:
+ $(XSUBPPRUN) $(XSPROTOARG) $(XSUBPPARGS) $(XSUBPP_EXTRA_ARGS) $*.xs > $*.xsc && $(MV) $*.xsc $*.c
+
+
+# --- MakeMaker xs_o section:
+
+.xs$(OBJ_EXT):
+ $(XSUBPPRUN) $(XSPROTOARG) $(XSUBPPARGS) $*.xs > $*.xsc && $(MV) $*.xsc $*.c
+ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c
+
+
+# --- MakeMaker top_targets section:
+all :: pure_all manifypods
+ $(NOECHO) $(NOOP)
+
+
+pure_all :: config pm_to_blib subdirs linkext
+ $(NOECHO) $(NOOP)
+
+subdirs :: $(MYEXTLIB)
+ $(NOECHO) $(NOOP)
+
+config :: $(FIRST_MAKEFILE) blibdirs
+ $(NOECHO) $(NOOP)
+
+$(O_FILES): $(H_FILES)
+
+help :
+ perldoc ExtUtils::MakeMaker
+
+
+# --- MakeMaker blibdirs section:
+blibdirs : $(INST_LIBDIR)$(DFSEP).exists $(INST_ARCHLIB)$(DFSEP).exists $(INST_AUTODIR)$(DFSEP).exists $(INST_ARCHAUTODIR)$(DFSEP).exists $(INST_BIN)$(DFSEP).exists $(INST_SCRIPT)$(DFSEP).exists $(INST_MAN1DIR)$(DFSEP).exists $(INST_MAN3DIR)$(DFSEP).exists
+ $(NOECHO) $(NOOP)
+
+# Backwards compat with 6.18 through 6.25
+blibdirs.ts : blibdirs
+ $(NOECHO) $(NOOP)
+
+$(INST_LIBDIR)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_LIBDIR)
+ $(NOECHO) $(CHMOD) 755 $(INST_LIBDIR)
+ $(NOECHO) $(TOUCH) $(INST_LIBDIR)$(DFSEP).exists
+
+$(INST_ARCHLIB)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_ARCHLIB)
+ $(NOECHO) $(CHMOD) 755 $(INST_ARCHLIB)
+ $(NOECHO) $(TOUCH) $(INST_ARCHLIB)$(DFSEP).exists
+
+$(INST_AUTODIR)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_AUTODIR)
+ $(NOECHO) $(CHMOD) 755 $(INST_AUTODIR)
+ $(NOECHO) $(TOUCH) $(INST_AUTODIR)$(DFSEP).exists
+
+$(INST_ARCHAUTODIR)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_ARCHAUTODIR)
+ $(NOECHO) $(CHMOD) 755 $(INST_ARCHAUTODIR)
+ $(NOECHO) $(TOUCH) $(INST_ARCHAUTODIR)$(DFSEP).exists
+
+$(INST_BIN)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_BIN)
+ $(NOECHO) $(CHMOD) 755 $(INST_BIN)
+ $(NOECHO) $(TOUCH) $(INST_BIN)$(DFSEP).exists
+
+$(INST_SCRIPT)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_SCRIPT)
+ $(NOECHO) $(CHMOD) 755 $(INST_SCRIPT)
+ $(NOECHO) $(TOUCH) $(INST_SCRIPT)$(DFSEP).exists
+
+$(INST_MAN1DIR)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_MAN1DIR)
+ $(NOECHO) $(CHMOD) 755 $(INST_MAN1DIR)
+ $(NOECHO) $(TOUCH) $(INST_MAN1DIR)$(DFSEP).exists
+
+$(INST_MAN3DIR)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_MAN3DIR)
+ $(NOECHO) $(CHMOD) 755 $(INST_MAN3DIR)
+ $(NOECHO) $(TOUCH) $(INST_MAN3DIR)$(DFSEP).exists
+
+
+
+# --- MakeMaker linkext section:
+
+linkext :: $(LINKTYPE)
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker dlsyms section:
+
+
+# --- MakeMaker dynamic section:
+
+dynamic :: $(FIRST_MAKEFILE) $(INST_DYNAMIC) $(INST_BOOT)
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker dynamic_bs section:
+BOOTSTRAP = $(BASEEXT).bs
+
+# As Mkbootstrap might not write a file (if none is required)
+# we use touch to prevent make continually trying to remake it.
+# The DynaLoader only reads a non-empty file.
+$(BOOTSTRAP) : $(FIRST_MAKEFILE) $(BOOTDEP) $(INST_ARCHAUTODIR)$(DFSEP).exists
+ $(NOECHO) $(ECHO) "Running Mkbootstrap for $(NAME) ($(BSLOADLIBS))"
+ $(NOECHO) $(PERLRUN) \
+ "-MExtUtils::Mkbootstrap" \
+ -e "Mkbootstrap('$(BASEEXT)','$(BSLOADLIBS)');"
+ $(NOECHO) $(TOUCH) $@
+ $(CHMOD) $(PERM_RW) $@
+
+$(INST_BOOT) : $(BOOTSTRAP) $(INST_ARCHAUTODIR)$(DFSEP).exists
+ $(NOECHO) $(RM_RF) $@
+ - $(CP) $(BOOTSTRAP) $@
+ $(CHMOD) $(PERM_RW) $@
+
+
+# --- MakeMaker dynamic_lib section:
+
+# This section creates the dynamically loadable $(INST_DYNAMIC)
+# from $(OBJECT) and possibly $(MYEXTLIB).
+ARMAYBE = :
+OTHERLDFLAGS =
+INST_DYNAMIC_DEP =
+INST_DYNAMIC_FIX =
+
+$(INST_DYNAMIC): $(OBJECT) $(MYEXTLIB) $(BOOTSTRAP) $(INST_ARCHAUTODIR)$(DFSEP).exists $(EXPORT_LIST) $(PERL_ARCHIVE) $(PERL_ARCHIVE_AFTER) $(INST_DYNAMIC_DEP)
+ $(RM_F) $@
+ $(LD) $(LDDLFLAGS) $(LDFROM) $(OTHERLDFLAGS) -o $@ $(MYEXTLIB) \
+ $(PERL_ARCHIVE) $(LDLOADLIBS) $(PERL_ARCHIVE_AFTER) $(EXPORT_LIST) \
+ $(INST_DYNAMIC_FIX)
+ $(CHMOD) $(PERM_RWX) $@
+
+
+# --- MakeMaker static section:
+
+## $(INST_PM) has been moved to the all: target.
+## It remains here for awhile to allow for old usage: "make static"
+static :: $(FIRST_MAKEFILE) $(INST_STATIC)
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker static_lib section:
+
+$(INST_STATIC) : $(OBJECT) $(MYEXTLIB) $(INST_ARCHAUTODIR)$(DFSEP).exists
+ $(RM_RF) $@
+ $(FULL_AR) $(AR_STATIC_ARGS) $@ $(OBJECT) && $(RANLIB) $@
+ $(CHMOD) $(PERM_RWX) $@
+ $(NOECHO) $(ECHO) "$(EXTRALIBS)" > $(INST_ARCHAUTODIR)/extralibs.ld
+
+
+# --- MakeMaker manifypods section:
+
+POD2MAN_EXE = $(PERLRUN) "-MExtUtils::Command::MM" -e pod2man "--"
+POD2MAN = $(POD2MAN_EXE)
+
+
+manifypods : pure_all \
+ CAlign.pm \
+ CAlign.pm
+ $(NOECHO) $(POD2MAN) --section=$(MAN3EXT) --perm_rw=$(PERM_RW) \
+ CAlign.pm $(INST_MAN3DIR)/Bio::Graphics::Browser::CAlign.$(MAN3EXT)
+
+
+
+
+# --- MakeMaker processPL section:
+
+
+# --- MakeMaker installbin section:
+
+
+# --- MakeMaker subdirs section:
+
+# none
+
+# --- MakeMaker clean_subdirs section:
+clean_subdirs :
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker clean section:
+
+# Delete temporary files but do not touch installed files. We don't delete
+# the Makefile here so a later make realclean still has a makefile to use.
+
+clean :: clean_subdirs
+ - $(RM_F) \
+ *$(LIB_EXT) core \
+ core.[0-9] $(INST_ARCHAUTODIR)/extralibs.all \
+ core.[0-9][0-9] $(BASEEXT).bso \
+ pm_to_blib.ts core.[0-9][0-9][0-9][0-9] \
+ $(BASEEXT).x $(BOOTSTRAP) \
+ perl$(EXE_EXT) tmon.out \
+ *$(OBJ_EXT) pm_to_blib \
+ $(INST_ARCHAUTODIR)/extralibs.ld blibdirs.ts \
+ core.[0-9][0-9][0-9][0-9][0-9] *perl.core \
+ core.*perl.*.? $(MAKE_APERL_FILE) \
+ perl $(BASEEXT).def \
+ core.[0-9][0-9][0-9] mon.out \
+ lib$(BASEEXT).def perlmain.c \
+ perl.exe CAlign.c \
+ so_locations $(BASEEXT).exp
+ - $(RM_RF) \
+ blib
+ - $(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD) $(DEV_NULL)
+
+
+# --- MakeMaker realclean_subdirs section:
+realclean_subdirs :
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker realclean section:
+# Delete temporary files (via clean) and also delete dist files
+realclean purge :: clean realclean_subdirs
+ - $(RM_F) \
+ $(OBJECT) $(MAKEFILE_OLD) \
+ $(FIRST_MAKEFILE)
+ - $(RM_RF) \
+ $(DISTVNAME)
+
+
+# --- MakeMaker metafile section:
+metafile : create_distdir
+ $(NOECHO) $(ECHO) Generating META.yml
+ $(NOECHO) $(ECHO) '# http://module-build.sourceforge.net/META-spec.html' > META_new.yml
+ $(NOECHO) $(ECHO) '#XXXXXXX This is a prototype!!! It will change in the future!!! XXXXX#' >> META_new.yml
+ $(NOECHO) $(ECHO) 'name: Bio-Graphics-Browser-CAlign' >> META_new.yml
+ $(NOECHO) $(ECHO) 'version: 1.00' >> META_new.yml
+ $(NOECHO) $(ECHO) 'version_from: CAlign.pm' >> META_new.yml
+ $(NOECHO) $(ECHO) 'installdirs: site' >> META_new.yml
+ $(NOECHO) $(ECHO) 'requires:' >> META_new.yml
+ $(NOECHO) $(ECHO) '' >> META_new.yml
+ $(NOECHO) $(ECHO) 'distribution_type: module' >> META_new.yml
+ $(NOECHO) $(ECHO) 'generated_by: ExtUtils::MakeMaker version 6.30_01' >> META_new.yml
+ -$(NOECHO) $(MV) META_new.yml $(DISTVNAME)/META.yml
+
+
+# --- MakeMaker signature section:
+signature :
+ cpansign -s
+
+
+# --- MakeMaker dist_basics section skipped.
+
+# --- MakeMaker dist_core section skipped.
+
+# --- MakeMaker distdir section skipped.
+
+# --- MakeMaker dist_test section skipped.
+
+# --- MakeMaker dist_ci section skipped.
+
+# --- MakeMaker distmeta section:
+distmeta : create_distdir metafile
+ $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{META.yml} => q{Module meta-data (added by MakeMaker)}}) } ' \
+ -e ' or print "Could not add META.yml to MANIFEST: $${'\''@'\''}\n"'
+
+
+
+# --- MakeMaker distsignature section:
+distsignature : create_distdir
+ $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{SIGNATURE} => q{Public-key signature (added by MakeMaker)}}) } ' \
+ -e ' or print "Could not add SIGNATURE to MANIFEST: $${'\''@'\''}\n"'
+ $(NOECHO) cd $(DISTVNAME) && $(TOUCH) SIGNATURE
+ cd $(DISTVNAME) && cpansign -s
+
+
+
+# --- MakeMaker install section skipped.
+
+# --- MakeMaker force section:
+# Phony target to force checking subdirectories.
+FORCE:
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker perldepend section:
+
+PERL_HDRS = \
+ $(PERL_INC)/EXTERN.h \
+ $(PERL_INC)/INTERN.h \
+ $(PERL_INC)/XSUB.h \
+ $(PERL_INC)/av.h \
+ $(PERL_INC)/cc_runtime.h \
+ $(PERL_INC)/config.h \
+ $(PERL_INC)/cop.h \
+ $(PERL_INC)/cv.h \
+ $(PERL_INC)/dosish.h \
+ $(PERL_INC)/embed.h \
+ $(PERL_INC)/embedvar.h \
+ $(PERL_INC)/fakethr.h \
+ $(PERL_INC)/form.h \
+ $(PERL_INC)/gv.h \
+ $(PERL_INC)/handy.h \
+ $(PERL_INC)/hv.h \
+ $(PERL_INC)/intrpvar.h \
+ $(PERL_INC)/iperlsys.h \
+ $(PERL_INC)/keywords.h \
+ $(PERL_INC)/mg.h \
+ $(PERL_INC)/nostdio.h \
+ $(PERL_INC)/op.h \
+ $(PERL_INC)/opcode.h \
+ $(PERL_INC)/patchlevel.h \
+ $(PERL_INC)/perl.h \
+ $(PERL_INC)/perlio.h \
+ $(PERL_INC)/perlsdio.h \
+ $(PERL_INC)/perlsfio.h \
+ $(PERL_INC)/perlvars.h \
+ $(PERL_INC)/perly.h \
+ $(PERL_INC)/pp.h \
+ $(PERL_INC)/pp_proto.h \
+ $(PERL_INC)/proto.h \
+ $(PERL_INC)/regcomp.h \
+ $(PERL_INC)/regexp.h \
+ $(PERL_INC)/regnodes.h \
+ $(PERL_INC)/scope.h \
+ $(PERL_INC)/sv.h \
+ $(PERL_INC)/thrdvar.h \
+ $(PERL_INC)/thread.h \
+ $(PERL_INC)/unixish.h \
+ $(PERL_INC)/util.h
+
+$(OBJECT) : $(PERL_HDRS)
+
+CAlign.c : $(XSUBPPDEPS)
+
+
+# --- MakeMaker makefile section:
+
+$(OBJECT) : $(FIRST_MAKEFILE)
+
+# We take a very conservative approach here, but it's worth it.
+# We move Makefile to Makefile.old here to avoid gnu make looping.
+$(FIRST_MAKEFILE) : Makefile.PL $(CONFIGDEP)
+ $(NOECHO) $(ECHO) "Makefile out-of-date with respect to $?"
+ $(NOECHO) $(ECHO) "Cleaning current config before rebuilding Makefile..."
+ -$(NOECHO) $(RM_F) $(MAKEFILE_OLD)
+ -$(NOECHO) $(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD)
+ - $(MAKE) $(USEMAKEFILE) $(MAKEFILE_OLD) clean $(DEV_NULL)
+ $(PERLRUN) Makefile.PL "DESTDIR=/tmp/tmp.fgGvra4059/unpdir/gbrowse-1.68/debian/gbrowse" "INSTALLDIRS=vendor" "VENDORARCHEXP=/usr/share/perl5"
+ $(NOECHO) $(ECHO) "==> Your Makefile has been rebuilt. <=="
+ $(NOECHO) $(ECHO) "==> Please rerun the $(MAKE) command. <=="
+ false
+
+
+
+# --- MakeMaker staticmake section:
+
+# --- MakeMaker makeaperl section ---
+MAP_TARGET = ../perl
+FULLPERL = /usr/bin/perl
+
+
+# --- MakeMaker test section:
+
+TEST_VERBOSE=0
+TEST_TYPE=test_$(LINKTYPE)
+TEST_FILE = test.pl
+TEST_FILES =
+TESTDB_SW = -d
+
+testdb :: testdb_$(LINKTYPE)
+
+test :: $(TEST_TYPE)
+
+test_dynamic :: pure_all
+ PERL_DL_NONLAZY=1 $(FULLPERLRUN) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
+
+testdb_dynamic :: pure_all
+ PERL_DL_NONLAZY=1 $(FULLPERLRUN) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
+
+test_ : test_dynamic
+
+test_static :: pure_all $(MAP_TARGET)
+ PERL_DL_NONLAZY=1 ./$(MAP_TARGET) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
+
+testdb_static :: pure_all $(MAP_TARGET)
+ PERL_DL_NONLAZY=1 ./$(MAP_TARGET) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
+
+
+
+# --- MakeMaker ppd section:
+# Creates a PPD (Perl Package Description) for a binary distribution.
+ppd:
+ $(NOECHO) $(ECHO) '<SOFTPKG NAME="$(DISTNAME)" VERSION="1,00,0,0">' > $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <TITLE>$(DISTNAME)</TITLE>' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <ABSTRACT>Compiled helper for Bio::Graphics::Browser::Realign</ABSTRACT>' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <AUTHOR>A. U. Thor <a.u.thor at a.galaxy.far.far.away></AUTHOR>' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <IMPLEMENTATION>' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <OS NAME="$(OSNAME)" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <ARCHITECTURE NAME="powerpc-linux-gnu-thread-multi" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' <CODEBASE HREF="" />' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) ' </IMPLEMENTATION>' >> $(DISTNAME).ppd
+ $(NOECHO) $(ECHO) '</SOFTPKG>' >> $(DISTNAME).ppd
+
+
+# --- MakeMaker pm_to_blib section:
+
+pm_to_blib : $(TO_INST_PM)
+ $(NOECHO) $(ABSPERLRUN) -MExtUtils::Install -e 'pm_to_blib({@ARGV}, '\''$(INST_LIB)/auto'\'', '\''$(PM_FILTER)'\'')' \
+ CAlign.pm $(INST_LIB)/Bio/Graphics/Browser/CAlign.pm
+ $(NOECHO) $(TOUCH) pm_to_blib
+
+
+# --- MakeMaker selfdocument section:
+
+
+# --- MakeMaker postamble section:
+
+
+# End.
Added: trunk/packages/gbrowse/trunk/pod2htmd.tmp
===================================================================
--- trunk/packages/gbrowse/trunk/pod2htmd.tmp (rev 0)
+++ trunk/packages/gbrowse/trunk/pod2htmd.tmp 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,16 @@
+docs/pod/
+.
+GBROWSE_IMG docs/pod//GBROWSE_IMG.pod:
+BIOSQL_ADAPTER_HOWTO docs/pod//BIOSQL_ADAPTER_HOWTO.pod:
+README-chado docs/pod//README-chado.pod:
+ORACLE_AND_POSTGRESQL docs/pod//ORACLE_AND_POSTGRESQL.pod:
+README-lucegene docs/pod//README-lucegene.pod:
+DAS_HOWTO docs/pod//DAS_HOWTO.pod:
+MAKE_IMAGES_HOWTO docs/pod//MAKE_IMAGES_HOWTO.pod:
+FAQ docs/pod//FAQ.pod:
+CONFIGURE_HOWTO docs/pod//CONFIGURE_HOWTO.pod:
+INSTALL.MacOSX docs/pod//INSTALL.MacOSX.pod:
+GENBANK_HOWTO docs/pod//GENBANK_HOWTO.pod:
+README-gff-files docs/pod//README-gff-files.pod:
+INSTALL docs/pod//INSTALL.pod:
+PLUGINS_HOWTO docs/pod//PLUGINS_HOWTO.pod:
Added: trunk/packages/gbrowse/trunk/pod2htmi.tmp
===================================================================
--- trunk/packages/gbrowse/trunk/pod2htmi.tmp (rev 0)
+++ trunk/packages/gbrowse/trunk/pod2htmi.tmp 2007-06-15 00:07:47 UTC (rev 329)
@@ -0,0 +1,2 @@
+docs/pod/
+.
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