Author: tille
Date: 2011-12-02 15:06:19 +0000 (Fri, 02 Dec 2011)
New Revision: 8748
Modified:
trunk/packages/ensembl/ensembl/trunk/debian/changelog
trunk/packages/ensembl/ensembl/trunk/debian/control
trunk/packages/ensembl/ensembl/trunk/debian/ensembl.links
trunk/packages/ensembl/ensembl/trunk/debian/prepare_ensembl_source_packages.sh
trunk/packages/ensembl/ensembl/trunk/debian/rules
Log:
Start fighting lintian problems, forther fixes in get-orig-source
Modified: trunk/packages/ensembl/ensembl/trunk/debian/changelog
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/changelog 2011-12-02
15:01:48 UTC (rev 8747)
+++ trunk/packages/ensembl/ensembl/trunk/debian/changelog 2011-12-02
15:06:19 UTC (rev 8748)
@@ -4,10 +4,18 @@
* debian/control:
- Fixed Vcs fields
- Added myself to uploaders
+ - Depends: tcsh|c-shell instead of csh and tcsh
+ - Do not depend from perl which is installed anyway
+ - Depends: jalview (and linked to jalview.jar in ensembl.links)
+ - Depends: jemboss (and linked to jalviewApplet.jar in ensembl.links)
+ - Internal dependencies always (= ${source:Version})
* debian/prepare_ensembl_source_packages.sh:
- Make sure the files that should be removed will be really removed
- Make script way less noisy
- Simplyfy script and move result to policy conform dir (./tarballs)
+ * debian/rules:
+ - use short dh with the same resulting package but a few less lintian
+ issues
-- Andreas Tille <[email protected]> Wed, 30 Nov 2011 13:30:15 +0100
Modified: trunk/packages/ensembl/ensembl/trunk/debian/control
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/control 2011-12-02 15:01:48 UTC
(rev 8747)
+++ trunk/packages/ensembl/ensembl/trunk/debian/control 2011-12-02 15:06:19 UTC
(rev 8748)
@@ -17,8 +17,25 @@
Package: ensembl
Architecture: all
Pre-Depends: debconf
-Depends: ${shlibs:Depends}, ${misc:Depends}, apache2-mpm-prefork, csh, expat,
perl, libcgi-pm-perl, libcgi-session-perl, libdb-file-lock-perl, libdbd-mysql,
perl-modules, ensembl-bin,
libensembl-core-perl,libensembl-functgenomics-perl,libensembl-compara-perl,libensembl-external-perl,libensembl-variation-perl,
tcsh, liblwp-parallel-perl, mysql-server, mysql-client
-Recommends: ttf-mscorefonts-installer, acedb-other-dotter, libcgi-ajax-perl,
libcache-memcached-perl, libclass-dbi-sweet-perl, libclass-std-perl,
libclass-std-utils-perl, libcompress-bzip2-perl, libfile-spec-perl,
libdata-uuid-libuuid-perl, libgd-text-perl, libhash-merge-perl,
libhtml-parser-perl, liblist-moreutils-perl, liblog-log4perl-perl,
libmailtools-perl, libwww-curl-perl, libapache2-mod-perl2,
libnumber-format-perl, libgd-gd2-noxpm-perl, libpdf-api2-perl,
libsys-hostname-long-perl, libtemplate-plugin-number-format-perl,
libxml-dom-perl, libxml-rss-perl, libxml-simple-perl, libbsd-resource-perl,
libxml-xpath-perl, libxml-atom-perl, libjson-perl,
libclass-data-inheritable-perl, libconfig-inifiles-perl,
libdevel-stacktrace-perl, libexception-class-perl, libhtml-template-perl,
libimage-size-perl, libio-string-perl, libipc-run-perl, libxml-libxml-perl,
libole-storage-lite-perl, libparse-recdescent-perl,
libspreadsheet-writeexcel-perl, libmime-types-perl, libmath-bezier-perl,
librtf-writer-perl, libbio-das-lite-perl, bioperl1.2.3|bioperl
+Depends: ${shlibs:Depends}, ${misc:Depends}, apache2-mpm-prefork,
tcsh|c-shell, expat,
+ libcgi-pm-perl, libcgi-session-perl, libdb-file-lock-perl, libdbd-mysql,
+ perl-modules, ensembl-bin, libensembl-core-perl,
libensembl-functgenomics-perl,
+ libensembl-compara-perl,libensembl-external-perl,libensembl-variation-perl,
+ liblwp-parallel-perl, mysql-server, mysql-client, jalview, jemboss
+Recommends: ttf-mscorefonts-installer, acedb-other-dotter, libcgi-ajax-perl,
+ libcache-memcached-perl, libclass-dbi-sweet-perl, libclass-std-perl,
+ libclass-std-utils-perl, libcompress-bzip2-perl, libfile-spec-perl,
+ libdata-uuid-libuuid-perl, libgd-text-perl, libhash-merge-perl,
libhtml-parser-perl,
+ liblist-moreutils-perl, liblog-log4perl-perl, libmailtools-perl,
libwww-curl-perl,
+ libapache2-mod-perl2, libnumber-format-perl, libgd-gd2-noxpm-perl,
libpdf-api2-perl,
+ libsys-hostname-long-perl, libtemplate-plugin-number-format-perl,
libxml-dom-perl,
+ libxml-rss-perl, libxml-simple-perl, libbsd-resource-perl, libxml-xpath-perl,
+ libxml-atom-perl, libjson-perl, libclass-data-inheritable-perl,
libconfig-inifiles-perl,
+ libdevel-stacktrace-perl, libexception-class-perl, libhtml-template-perl,
+ libimage-size-perl, libio-string-perl, libipc-run-perl, libxml-libxml-perl,
+ libole-storage-lite-perl, libparse-recdescent-perl,
libspreadsheet-writeexcel-perl,
+ libmime-types-perl, libmath-bezier-perl, librtf-writer-perl,
libbio-das-lite-perl,
+ bioperl1.2.3|bioperl
Suggests: ksh | mksh | pdksh | zsh
Section: non-free/science
Description: basic Ensembl genome browser
@@ -92,7 +109,7 @@
hypoxia, temperature changes, growth, ...) and of course in diseases.
Package: libensembl-compara-perl
-Depends: ${misc:Depends},libensembl-core-perl
+Depends: ${misc:Depends}, libensembl-core-perl (= ${source:Version})
Architecture: all
Section: non-free/perl
Description: API for comparative genomics with Ensembl
@@ -110,7 +127,7 @@
changed mean something?
Package: libensembl-external-perl
-Depends: ${misc:Depends},libensembl-core-perl
+Depends: ${misc:Depends}, libensembl-core-perl (= ${source:Version})
Architecture: all
Section: non-free/perl
Description: API for integration of external data sources with Ensembl
@@ -124,7 +141,7 @@
pacakges.
Package: libensembl-variation-perl
-Depends: ${misc:Depends},libensembl-core-perl
+Depends: ${misc:Depends}, libensembl-core-perl (= ${source:Version})
Architecture: all
Section: non-free/perl
Description: Ensembl API for investigation of inter-individual genomic
differences
@@ -140,7 +157,7 @@
and may generate ideas for novel drugs at best.
Package: libensembl-draw-perl
-Depends: ${misc:Depends},libensembl-core-perl
+Depends: ${misc:Depends}, libensembl-core-perl (= ${source:Version})
Architecture: all
Section: non-free/perl
Description: Ensembl API for graphical representation of genomic properties
Modified: trunk/packages/ensembl/ensembl/trunk/debian/ensembl.links
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/ensembl.links 2011-12-02
15:01:48 UTC (rev 8747)
+++ trunk/packages/ensembl/ensembl/trunk/debian/ensembl.links 2011-12-02
15:06:19 UTC (rev 8748)
@@ -1,3 +1,5 @@
+/usr/share/java/jalview.jar
/usr/share/ensembl/htdocs/jalview/jalview.jar
+/usr/share/EMBOSS/jemboss/lib/jalviewApplet.jar
/usr/share/ensembl/htdocs/jalview/jalviewApplet.jar
#Commented because tried to do it here but didn't work, so
# we are using postinst instead
#/usr/share/ensembl/logs /var/log/ensembl
Modified:
trunk/packages/ensembl/ensembl/trunk/debian/prepare_ensembl_source_packages.sh
===================================================================
---
trunk/packages/ensembl/ensembl/trunk/debian/prepare_ensembl_source_packages.sh
2011-12-02 15:01:48 UTC (rev 8747)
+++
trunk/packages/ensembl/ensembl/trunk/debian/prepare_ensembl_source_packages.sh
2011-12-02 15:06:19 UTC (rev 8748)
@@ -18,6 +18,8 @@
grep "Newest version on remote site is .* local version is .*"
| \
head -n 1 | \
sed "s/Newest version on remote site is \([-0-9.]\+\),.*/\1/"`
+ # remove fake download file again
+ rm -f ../release-$ensemblversion
else
# If called by uscan
ensemblversion=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\)
.*${PKG}.*?\1?"`
@@ -38,7 +40,6 @@
mkdir -p "$downloaddir"
cd "$downloaddir"
-##if [ 1 = 0 ] ; then ## debug
export CVSROOT=":pserver:[email protected]:/cvsroot/ensembl"
echo " * Logging in to Sanger CVS, type password CVSUSER"
@@ -55,11 +56,10 @@
fi
echo
done
-##fi # end debug
# set -x
-# still in $downloaddir
find . -name CVS -a -type d | xargs -r rm -rf
+find . -name .cvsignore -type f -delete
# Removing a series of files for better DFSG compliance
find . -name "*.pdf" | grep -v ComparaTutorial | xargs -r rm
Modified: trunk/packages/ensembl/ensembl/trunk/debian/rules
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/rules 2011-12-02 15:01:48 UTC
(rev 8747)
+++ trunk/packages/ensembl/ensembl/trunk/debian/rules 2011-12-02 15:06:19 UTC
(rev 8748)
@@ -1,48 +1,34 @@
#!/usr/bin/make -f
# -*- makefile -*-
-# Sample debian/rules that uses debhelper.
-# This file was originally written by Joey Hess and Craig Small.
-# As a special exception, when this file is copied by dh-make into a
-# dh-make output file, you may use that output file without restriction.
-# This special exception was added by Craig Small in version 0.37 of dh-make.
+# debian/rules for ensembl using dh
+# Author: Andreas Tille
+# License: GPL
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
DESTDIR=$(CURDIR)/debian/ensembl
-configure: configure-stamp
-configure-stamp:
- # nothing to be configured
- touch configure-stamp
+%:
+ dh $@
-# Ignoring direct call to build
-build: #build-indep-stamp build-arch
- echo "Build command ignored. Ask for a binary."
-
-build-arch: ensembl-variation/C_code/calc_genotypes
-ensembl-variation/C_code/calc_genotypes:
+override_dh_auto_build:
+ # build-arch
$(MAKE) -C ensembl-variation/C_code calc_genotypes
-build-indep: build-indep-stamp
-build-indep-stamp:
+ # build-indep
# nothing to build for the Perl packages or the database
- # well, those bits should already have been fixed in the source tree,
but, who knows...
- find . -name CVS -a -type d | xargs -r rm -r
find . -name "*.pm" -o -name "*.png" -o -name "*.gif" -o -name README \
-o -name "*.sql" -o -name "*.pdf" -o -name "*.html" \
-o -name "*.sxw" -o -name "*.conf*" -o -name "*.guess" -o -name
"*.sub" \
-o -name "*.h" -o -name "*.cpp" -o -name "*.txt" \
| grep -v "/.pc/" | xargs -r --max-args 10
chmod 644
- #find . -name "*.pl" | xargs -r chmod 755
- find . -name ".cvsignore" | xargs -r rm
# First round of updates
find . -name "*.pl" -o -name "*.sh" -o -name "*.t" -o -name "*.pm" -o \
-name "do_flatfile_dump_registry" -o -name
"parse_snp_to_ensembl_mouse" \
| grep -v "/.pc/" | xargs -r --max-args 1
debian/adjust_shebang_line.sh
- #d=$(DESTDIR)/usr/share/ensembl
echo "Adjusting path to Perl wherever it may be found" ; \
egrep -rl "^#!\s*/.*/perl" . | grep -v "/.pc/" | xargs -r --max-args 1
sed -i '1s%^#!\s*/\(usr\|localsw\)/.*/perl%#!/usr/bin/perl%' ; \
egrep -rl "^#!\s*/.*/perl" . | grep -v "/.pc/" | xargs -r --max-args 1
sed -i '1s%^#!\s*/\(usr\|localsw\|software\)/.*/perl%#!/usr/bin/perl%' ; \
@@ -50,37 +36,9 @@
egrep -rl "^#!\s*/.*/bash" . | grep -v "/.pc/" | xargs -r --max-args 1
sed -i '1s%^#!\s*/\(usr\|localsw\)/.*/bash%#!/bin/bash%' ; \
egrep -rl "^#!.*ENV.*PERL" . | grep -v "/.pc/" | xargs -r --max-args 1
sed -i '1s%^#!.*%#!/usr/bin/perl%' ; \
- # First round of updates
- #find . -name "*.pl" -o -name "*.sh" | xargs -r debian/adjust_chmod.sh
- touch $@
-
-install-arch: build-arch
- dh_testdir
- dh_testroot
- dh_prep -a
- dd="$(DESTDIR)-bin/usr/bin" ; \
- if [ ! -d "$$$d" ]; then \
- echo "Creating directory '$$dd'." ; \
- mkdir -p "$$dd" ; \
- fi ; \
- cp ensembl-variation/C_code/calc_genotypes $$dd
-
-install-indep: build-indep install-indep-copying
- # copying files that are considered too different from the original
- # and/or the original too variable across releases to be patched
- if [ ! -d "$(DESTDIR)/etc/default/ensembl.d" ]; then mkdir -p
"$(DESTDIR)/etc/default/ensembl.d"; fi
- cp debian/ensembl.overwrites/Plugins.pm
"$(DESTDIR)/etc/default/ensembl.d/"
- cp debian/ensembl.overwrites/confSiteDefs.pm
"$(DESTDIR)/etc/default/ensembl.d/"
- cp debian/ensembl.overwrites/pluginSiteDefs.pm
"$(DESTDIR)/etc/default/ensembl.d/"
- find debian/ensembl -name config.guess -o -name config.sub -o -name
configure -o \
- -name depcomp -o -name install-sh -o -name missing -o -name
Makefile.PL | xargs -r rm
-
-install-indep-copying: install-indep-copying-stamp
-install-indep-copying-stamp:
- dh_testdir
- dh_testroot
- dh_prep -i
+override_dh_auto_install:
+ # install-arch
d="$(DESTDIR)/usr/share/ensembl" ; \
if [ ! -d "$$d" ]; then \
echo "Creating directory '$$d'." ; \
@@ -100,7 +58,7 @@
docdirbase=`basename $$docdir` ; \
from="$(DESTDIR)/usr/share/ensembl/$$docdirbase/docs" ; \
to="$$m/$$docdirbase" ; \
- echo "Moving from '$$from' to '$$to'.\n" ; \
+ # echo "Moving from '$$from' to '$$to'.\n" ; \
mv "$$from" "$$to" ; \
done
@@ -111,7 +69,7 @@
from="debian/ensembl/usr/share/ensembl/ensembl" ; \
to="debian/libensembl-core-perl/usr/share/ensembl/" ; \
- echo "Renaming '$$from' to '$$to'.\n" ; \
+ # echo "Renaming '$$from' to '$$to'.\n" ; \
mv "$$from" "$$to"
# move the remaining directories
@@ -126,47 +84,34 @@
find debian -name Makefile.PL -o -name "*.tar.gz" | xargs -r rm -f
rm -rf
debian/libensembl-variation-perl/usr/share/ensembl/ensembl-variation/C_code
-clean:
+ dd="$(DESTDIR)-bin/usr/bin" ; \
+ if [ ! -d "$$$d" ]; then \
+ echo "Creating directory '$$dd'." ; \
+ mkdir -p "$$dd" ; \
+ fi ; \
+ cp ensembl-variation/C_code/calc_genotypes $$dd
+
+ # install-indep: build-indep install-indep-copying
+ # copying files that are considered too different from the original
+ # and/or the original too variable across releases to be patched
+ if [ ! -d "$(DESTDIR)/etc/default/ensembl.d" ]; then mkdir -p
"$(DESTDIR)/etc/default/ensembl.d"; fi
+ cp debian/ensembl.overwrites/Plugins.pm
"$(DESTDIR)/etc/default/ensembl.d/"
+ cp debian/ensembl.overwrites/confSiteDefs.pm
"$(DESTDIR)/etc/default/ensembl.d/"
+ cp debian/ensembl.overwrites/pluginSiteDefs.pm
"$(DESTDIR)/etc/default/ensembl.d/"
+ find debian/ensembl -name config.guess -o -name config.sub -o -name
configure -o \
+ -name depcomp -o -name install-sh -o -name missing -o -name
Makefile.PL | xargs -r rm
+
+override_dh_auto_clean:
+ dh_auto_clean
rm -f ensembl-variation/C_code/calc_genotypes.o
ensembl-variation/C_code/calc_genotypes
debconf-updatepo
dh_clean install-indep-copying-stamp \
build-stamp build-indep-stamp build-arch-stamp \
configure-stamp
-binary-common:
- dh_testdir
- dh_testroot
- dh_installchangelogs
- dh_installdebconf
- dh_installdocs
- dh_installexamples
- dh_install
- dh_installman
- dh_installinit
- dh_link
- dh_strip
- dh_compress
- dh_fixperms
- dh_perl
- dh_installdeb
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-
-binary-indep: install-indep
- $(MAKE) -f debian/rules DH_OPTIONS=-i binary-common
-
-# Build architecture dependant packages using the common target.
-binary-arch: install-arch
- $(MAKE) -f debian/rules DH_OPTIONS=-s binary-common
-
-binary: binary-arch binary-indep
-
get-orig-source:
./debian/prepare_ensembl_source_packages.sh
# To update po files as recommended in po-debconf(7)
debian/po/templates.pot: debian/ensembl.templates
@debconf-updatepo
-
-.PHONY: build clean binary-indep binary-arch binary configure build install
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