[med-svn] r338 - in trunk/packages/gbrowse/trunk: . debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Tue Jun 19 05:20:35 UTC 2007
Author: charles-guest
Date: 2007-06-19 05:20:35 +0000 (Tue, 19 Jun 2007)
New Revision: 338
Removed:
trunk/packages/gbrowse/trunk/Makefile.old
trunk/packages/gbrowse/trunk/bin/
trunk/packages/gbrowse/trunk/conf/
trunk/packages/gbrowse/trunk/libalign/
trunk/packages/gbrowse/trunk/pod2htmd.tmp
trunk/packages/gbrowse/trunk/pod2htmi.tmp
Modified:
trunk/packages/gbrowse/trunk/debian/control
Log:
Cleaning; adding SVN info.
Deleted: trunk/packages/gbrowse/trunk/Makefile.old
===================================================================
--- trunk/packages/gbrowse/trunk/Makefile.old 2007-06-18 08:36:10 UTC (rev 337)
+++ trunk/packages/gbrowse/trunk/Makefile.old 2007-06-19 05:20:35 UTC (rev 338)
@@ -1,1392 +0,0 @@
-# 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) $(INST_SCRIPT)/register_moby_services.pl
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-$(INST_SCRIPT)/process_gadfly.pl : bin/process_gadfly.pl $(FIRST_MAKEFILE) $(INST_SCRIPT)$(DFSEP).exists $(INST_BIN)$(DFSEP).exists
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- 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.
Modified: trunk/packages/gbrowse/trunk/debian/control
===================================================================
--- trunk/packages/gbrowse/trunk/debian/control 2007-06-18 08:36:10 UTC (rev 337)
+++ trunk/packages/gbrowse/trunk/debian/control 2007-06-19 05:20:35 UTC (rev 338)
@@ -5,10 +5,13 @@
Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>
Build-Depends: debhelper (>= 5), bioperl (>= 1.5.2), quilt
Standards-Version: 3.7.2
+XS-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gbrowse/trunk/
+XS-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/gbrowse
Package: gbrowse
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Architecture: all
+Depends: libcgi-session-perl, ${shlibs:Depends}, ${misc:Depends}
+Recommends: libdbd-mysql-perl, libdb4.4
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
Deleted: trunk/packages/gbrowse/trunk/pod2htmd.tmp
===================================================================
--- trunk/packages/gbrowse/trunk/pod2htmd.tmp 2007-06-18 08:36:10 UTC (rev 337)
+++ trunk/packages/gbrowse/trunk/pod2htmd.tmp 2007-06-19 05:20:35 UTC (rev 338)
@@ -1,16 +0,0 @@
-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:
Deleted: trunk/packages/gbrowse/trunk/pod2htmi.tmp
===================================================================
--- trunk/packages/gbrowse/trunk/pod2htmi.tmp 2007-06-18 08:36:10 UTC (rev 337)
+++ trunk/packages/gbrowse/trunk/pod2htmi.tmp 2007-06-19 05:20:35 UTC (rev 338)
@@ -1,2 +0,0 @@
-docs/pod/
-.
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