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 <[EMAIL PROTECTED]> DM-Upload-Allowed: yes Uploaders: Charles Plessy <[EMAIL PROTECTED]> -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 <[EMAIL PROTECTED]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
