[med-svn] r2486 - in trunk/packages/gbrowse/trunk/debian: . patches
plessy at alioth.debian.org
plessy at alioth.debian.org
Fri Sep 12 07:31:57 UTC 2008
Author: plessy
Date: 2008-09-12 07:31:55 +0000 (Fri, 12 Sep 2008)
New Revision: 2486
Added:
trunk/packages/gbrowse/trunk/debian/apache.conf
trunk/packages/gbrowse/trunk/debian/gbrowse.links
trunk/packages/gbrowse/trunk/debian/install
Modified:
trunk/packages/gbrowse/trunk/debian/compat
trunk/packages/gbrowse/trunk/debian/control
trunk/packages/gbrowse/trunk/debian/patches/series
trunk/packages/gbrowse/trunk/debian/rules
Log:
Work in progress. Upstream will modify the build system to ease our work.
(For the moment, some paths are hardcoded to the $(TMP) directory when
make install is called).
Added: trunk/packages/gbrowse/trunk/debian/apache.conf
===================================================================
--- trunk/packages/gbrowse/trunk/debian/apache.conf (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/apache.conf 2008-09-12 07:31:55 UTC (rev 2486)
@@ -0,0 +1,13 @@
+# I used /etc/gallery2/apache.conf as a template. -- Charles Plessy
+Alias /gbrowse /usr/share/gbrowse
+
+<Directory /usr/share/gbrowse>
+ Options FollowSymLinks
+# AllowOverride Limit Options FileInfo
+</Directory>
+
+# some people prefer a simple URL like http://gbrowse.example
+#<VirtualHost *:80>
+# DocumentRoot /usr/share/gbrowse
+# ServerName gbrowse.example
+#</VirtualHost>
Modified: trunk/packages/gbrowse/trunk/debian/compat
===================================================================
--- trunk/packages/gbrowse/trunk/debian/compat 2008-09-12 07:00:18 UTC (rev 2485)
+++ trunk/packages/gbrowse/trunk/debian/compat 2008-09-12 07:31:55 UTC (rev 2486)
@@ -1 +1 @@
-5
+7
Modified: trunk/packages/gbrowse/trunk/debian/control
===================================================================
--- trunk/packages/gbrowse/trunk/debian/control 2008-09-12 07:00:18 UTC (rev 2485)
+++ trunk/packages/gbrowse/trunk/debian/control 2008-09-12 07:31:55 UTC (rev 2486)
@@ -4,7 +4,7 @@
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <plessy at debian.org>
-Build-Depends: debhelper (>= 5), bioperl (>= 1.5.2), quilt
+Build-Depends: debhelper (>= 7), bioperl (> 1.5.2), quilt
Standards-Version: 3.7.3
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gbrowse/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/gbrowse/trunk/
@@ -12,8 +12,11 @@
Package: gbrowse
Architecture: all
-Depends: libcgi-session-perl, libtext-shellwords-perl, ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Perl}
+ libclass-base-perl, libio-string-perl, bioperl, libcgi-session-perl, libgd-gd2-noxpm-perl, libstatistics-descriptive-perl
+# The above line comes from dh-make-perl
Recommends: libdbd-mysql-perl, libdb4.4
+# Should probably also recomment mod-perl
Description: The generic genome browser component of the GMOD project
The 'generic genome browser' component of the Generic Model Organism Database
toolkit (GMOD) is a combination of database and interactive Web page for
Added: trunk/packages/gbrowse/trunk/debian/gbrowse.links
===================================================================
--- trunk/packages/gbrowse/trunk/debian/gbrowse.links (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/gbrowse.links 2008-09-12 07:31:55 UTC (rev 2486)
@@ -0,0 +1 @@
+etc/gbrowse.conf/apache.conf etc/apache2/conf.d/gbrowse
Added: trunk/packages/gbrowse/trunk/debian/install
===================================================================
--- trunk/packages/gbrowse/trunk/debian/install (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/install 2008-09-12 07:31:55 UTC (rev 2486)
@@ -0,0 +1 @@
+debian/apache.conf etc/gbrowse.conf
Modified: trunk/packages/gbrowse/trunk/debian/patches/series
===================================================================
--- trunk/packages/gbrowse/trunk/debian/patches/series 2008-09-12 07:00:18 UTC (rev 2485)
+++ trunk/packages/gbrowse/trunk/debian/patches/series 2008-09-12 07:31:55 UTC (rev 2486)
@@ -1 +1 @@
-blast2gff_1.69-and-usrbin.patch
+#blast2gff_1.69-and-usrbin.patch
Modified: trunk/packages/gbrowse/trunk/debian/rules
===================================================================
--- trunk/packages/gbrowse/trunk/debian/rules 2008-09-12 07:00:18 UTC (rev 2485)
+++ trunk/packages/gbrowse/trunk/debian/rules 2008-09-12 07:31:55 UTC (rev 2486)
@@ -1,90 +1,95 @@
#!/usr/bin/make -f
-# -*- makefile -*-
+# This debian/rules file is provided as a template for normal perl
+# packages. It was created by Marc Brockschmidt <marc at dch-faq.de> for
+# the Debian Perl Group (http://pkg-perl.alioth.debian.org/) but may
+# be used freely wherever it is useful.
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
include /usr/share/quilt/quilt.make
-configure: configure-stamp
-configure-stamp:
- dh_testdir
- perl Makefile.PL \
- DESTDIR=/usr \
- CGIBIN=/usr/lib/cgi-bin \
- CONF=/etc/ \
- HTDOCS=/var/www \
- INSTALLDIRS=vendor \
- VENDORARCHEXP=/usr/share/perl5
- touch configure-stamp
+# If set to a true value then MakeMaker's prompt function will
+# always return the default without waiting for user input.
+export PERL_MM_USE_DEFAULT=1
+PERL ?= /usr/bin/perl
+PACKAGE = $(shell dh_listpackages)
+TMP = $(CURDIR)/debian/$(PACKAGE)
+
+# Allow disabling build optimisation by setting noopt in
+# $DEB_BUILD_OPTIONS
+CFLAGS = -Wall -g
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
build: patch build-stamp
-build-stamp: configure-stamp
+build-stamp:
dh_testdir
- $(MAKE) OPTIMIZE="-O2 -g -Wall"
+ # Add commands to compile the package here
+ $(PERL) Makefile.PL \
+ INSTALLDIRS=vendor \
+ APACHE=/etc/apache2 \
+ CONF=/etc \
+ CGIBIN=/usr/lib/cgi-bin \
+ HTDOCS=/usr/share \
+ DO_XS=1
+ $(MAKE) OPTIMIZE="$(CFLAGS)" LD_RUN_PATH=""
+ $(MAKE) test
touch $@
-clean: unpatch configure-stamp
+clean: unpatch
dh_testdir
dh_testroot
- rm -f build-stamp configure-stamp
- $(MAKE) clean
- dh_clean
+ dh_clean build-stamp install-stamp
+ # Add commands to clean up after the build process here
+ [ ! -f Makefile ] || $(MAKE) realclean
-install: build
- perl Makefile.PL \
- DESTDIR=$(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
+install: install-stamp
+install-stamp: build-stamp
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 fix to get correct path
- perl -i -pe 's:$(CURDIR)/gbrowse/etc//gbrowse.conf:/etc/gbrowse.conf:' debian/gbrowse/usr/lib/cgi-bin/*
-
- # Add programs in /usr/bin
- cp contrib/blast2gff.pl $(CURDIR)/debian/gbrowse/usr/bin/blast2gff
- perldoc $(CURDIR)/debian/gbrowse/usr/bin/blast2gff > $(CURDIR)/debian/gbrowse/usr/share/man/man1/blast2gff.1
-
+ dh_clean -k
+ # Add commands to install the package into $(TMP)
+ $(PERL) Makefile.PL \
+ INSTALLDIRS=vendor \
+ APACHE=$(TMP)/etc/apache2 \
+ CONF=$(TMP)/etc \
+ CGIBIN=$(TMP)/usr/lib/cgi-bin \
+ HTDOCS=$(TMP)/usr/share/ \
+ DO_XS=1
+ $(MAKE) install DESTDIR=$(TMP) PREFIX=/usr
+ [ ! -d $(TMP)/usr/share/perl5 ] || \
+ rmdir --ignore-fail-on-non-empty --parents --verbose \
+ $(TMP)/usr/share/perl5
# UGLY WORKAROUND TO A CONFLICT WITH BIOPERL 1.5.2
- rm $(CURDIR)/debian/gbrowse/usr/share/man/man3/Bio::Graphics::FeatureFile.3pm
+ rm $(TMP)/usr/share/man/man3/Bio::Graphics::Glyph::ideogram.3pm
+ rm $(TMP)/usr/share/man/man3/Bio::Graphics::Glyph::heat_map.3pm
+ rm $(TMP)/usr/share/man/man3/Bio::Graphics::Glyph::heat_map_ideogram.3pm
+ touch $@
+# Build architecture-independent files here.
binary-indep: build install
+# We have nothing to do here for an architecture-dependent package
+# Build architecture-dependent files here.
binary-arch: build install
dh_testdir
dh_testroot
+ dh_installdocs
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_shlibdeps
dh_strip
+ dh_perl
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
+.PHONY: build clean binary-indep binary-arch binary install
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