Author: tille Date: 2015-03-04 13:12:01 +0000 (Wed, 04 Mar 2015) New Revision: 18903
Added: trunk/packages/spades/trunk/debian/docs trunk/packages/spades/trunk/debian/install Removed: trunk/packages/spades/trunk/debian/patches/use-debian-packaged-bwa.patch Modified: trunk/packages/spades/trunk/debian/control trunk/packages/spades/trunk/debian/copyright trunk/packages/spades/trunk/debian/links trunk/packages/spades/trunk/debian/patches/series trunk/packages/spades/trunk/debian/rules Log: Get something that somehow builds and passes the test. Keep on with the replacement of code copies Modified: trunk/packages/spades/trunk/debian/control =================================================================== --- trunk/packages/spades/trunk/debian/control 2015-03-04 08:51:09 UTC (rev 18902) +++ trunk/packages/spades/trunk/debian/control 2015-03-04 13:12:01 UTC (rev 18903) @@ -9,9 +9,12 @@ zlib1g-dev, libbz2-dev, libboost-dev, + libbam-dev, libbamtools-dev, libhts-dev, - lynx + python-yaml, + python-joblib, + bwa Standards-Version: 3.9.6 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/spades/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/spades/trunk/ Modified: trunk/packages/spades/trunk/debian/copyright =================================================================== --- trunk/packages/spades/trunk/debian/copyright 2015-03-04 08:51:09 UTC (rev 18902) +++ trunk/packages/spades/trunk/debian/copyright 2015-03-04 13:12:01 UTC (rev 18903) @@ -3,23 +3,22 @@ Upstream-Contact: spades.supp...@bioinf.spbau.ru Source: http://spades.bioinf.spbau.ru/ Files-Excluded: - ext/include/boost ext/src/python_libs - ext/tools/bwa-0.6.2 - ext/*/bamtools - ext/*/samtools/samtools - ext/*/samtools/misc/ace2sam - ext/*/samtools/misc/bamcheck - ext/*/samtools/misc/maq2sam-* - ext/*/samtools/misc/md5fa - ext/*/samtools/misc/md5sum-lite - ext/*/samtools/misc/wgsim - ext/*/samtools/bcftools/bcftools - ext/*/samtools/win32 + ext/tools/bwa-* + ext/include/samtools + ext/src/samtools/samtools + ext/src/samtools/misc/ace2sam + ext/src/samtools/misc/bamcheck + ext/src/samtools/misc/maq2sam-* + ext/src/samtools/misc/md5fa + ext/src/samtools/misc/md5sum-lite + ext/src/samtools/misc/wgsim + ext/src/samtools/bcftools/bcftools + ext/src/samtools/win32 Files: * Copyright: 2011-2013 Saint-Petersburg Academic University -License: GPLv2+ +License: GPL-2 Files: ext/include/ConsensusCore/* Copyright: 2011-2013, Pacific Biosciences of California, Inc. @@ -59,17 +58,11 @@ It might make sense to package this for Debian separately since it is in the field of Debian Med -Files: ext/include/otkpp/* -Copyright: pulkk...@gmail.com -License: GPLv3+ -Comment: This is a code copy from - http://code.google.com/p/otkpp/ - Files: debian/* Copyright: 2014 Andreas Tille <ti...@debian.org> -License: GPLv2+ +License: GPL-2 -License: GPLv2+ +License: GPL-2 This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or @@ -87,7 +80,7 @@ On Debian systems you can find the full test of the GNU General Public License version 2 at /usr/share/common-licenses/GPL-2. -License: GPLv3+ +License: GPL-3 This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or Added: trunk/packages/spades/trunk/debian/docs =================================================================== --- trunk/packages/spades/trunk/debian/docs (rev 0) +++ trunk/packages/spades/trunk/debian/docs 2015-03-04 13:12:01 UTC (rev 18903) @@ -0,0 +1 @@ +*manual.html Added: trunk/packages/spades/trunk/debian/install =================================================================== --- trunk/packages/spades/trunk/debian/install (rev 0) +++ trunk/packages/spades/trunk/debian/install 2015-03-04 13:12:01 UTC (rev 18903) @@ -0,0 +1 @@ +install_spades/* usr Modified: trunk/packages/spades/trunk/debian/links =================================================================== --- trunk/packages/spades/trunk/debian/links 2015-03-04 08:51:09 UTC (rev 18902) +++ trunk/packages/spades/trunk/debian/links 2015-03-04 13:12:01 UTC (rev 18903) @@ -1,3 +1,5 @@ -usr/bin/spades usr/bin/dipspades -usr/lib/spades/share/spades/test_dataset usr/share/doc/spades/examples -usr/bin/bwa usr/lib/spades/bin/bwa-spades +#usr/bin/spades usr/bin/dipspades +#usr/lib/spades/share/spades/test_dataset usr/share/doc/spades/examples +#usr/bin/bwa usr/bin/bwa-spades +#etc/spades usr/share/spades/configs +#usr/share usr/lib/spades/share Modified: trunk/packages/spades/trunk/debian/patches/series =================================================================== --- trunk/packages/spades/trunk/debian/patches/series 2015-03-04 08:51:09 UTC (rev 18902) +++ trunk/packages/spades/trunk/debian/patches/series 2015-03-04 13:12:01 UTC (rev 18903) @@ -3,8 +3,8 @@ 0003_accept-system-bwa.patch 0101_cmake_ignore_removed_python-yaml.patch 0102_cmake_ignore_removed_python-joblib.patch +0103_use-debian-packaged-bwa.patch #do_not_install_third_party_libs.patch #adapt_to_debian_pathes.patch -use-debian-packaged-bwa.patch # use-debian-packaged-samtools.patch # bamtools-cmake.patch Deleted: trunk/packages/spades/trunk/debian/patches/use-debian-packaged-bwa.patch =================================================================== --- trunk/packages/spades/trunk/debian/patches/use-debian-packaged-bwa.patch 2015-03-04 08:51:09 UTC (rev 18902) +++ trunk/packages/spades/trunk/debian/patches/use-debian-packaged-bwa.patch 2015-03-04 13:12:01 UTC (rev 18903) @@ -1,22 +0,0 @@ -Author: Andreas Tille <ti...@debian.org> -Last-Changed: Tue, 18 Feb 2014 15:48:55 +0100 -Description: SPAdes originally contained a code copy of bwa since the version - of bwa which was current of the time of release did not builded with recent - gcc versions. Since this is not the case with Debian shipped bwa this code - copy is skipped. - . - See https://lists.debian.org/debian-med/2014/02/msg00192.html - . - Note: I tried to patch the Python scripts which were calling bwa-spades to - rather call /usr/bin/bwa but the test suite failed. So as an alternative - the package contains a symlink - ln -s /usr/bin/bwa /usr/lib/spades/bin/bwa-spades - which enables successfull run of the test suite - ---- a/ext/tools/CMakeLists.txt -+++ b/ext/tools/CMakeLists.txt -@@ -4,4 +4,3 @@ - # See file LICENSE for details. - ############################################################################ - --add_subdirectory(bwa-0.6.2) Modified: trunk/packages/spades/trunk/debian/rules =================================================================== --- trunk/packages/spades/trunk/debian/rules 2015-03-04 08:51:09 UTC (rev 18902) +++ trunk/packages/spades/trunk/debian/rules 2015-03-04 13:12:01 UTC (rev 18903) @@ -3,30 +3,49 @@ # DH_VERBOSE := 1 DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') -LIBDIR := debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME) -SHAREDIR := debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME) +TMPDIR := $(CURDIR)/install_spades PREFIX:=/usr -BUILD_DIR:=build_spades +BUILD_DIR:=$(CURDIR)/build_spades DEB_CMAKE_EXTRA_FLAGS = -DSPADES_BOOST_ROOT=/usr/include %: dh $@ --with python2 --sourcedirectory=src --buildsystem=cmake +override_dh_auto_clean: + dh_auto_clean + rm -rf build_spades + rm -rf install_spades + rm -rf spades_test + find . -name "*.pyc" -delete + +override_dh_auto_configure: + echo "Simply use spades_compile.sh in auto_build" + +override_dh_auto_build: + PREFIX=$(TMPDIR) ./spades_compile.sh + +override_dh_auto_test: + $(TMPDIR)/bin/spades.py --test + +override_dh_auto_install: + echo "Nothing to install" + override_dh_install: + dh_install # move those binaries away from /usr/bin that do not need to be called explicitly - mkdir -p $(LIBDIR) - mv debian/$(DEBPKGNAME)/usr/bin $(LIBDIR) + #mkdir -p $(LIBDIR) + #mv debian/$(DEBPKGNAME)/usr/bin $(LIBDIR) #mkdir -p $(LIBDIR)/share #mv $(SHAREDIR) $(LIBDIR)/share - for pyfile in `ls $(LIBDIR)/bin/*.py` ; do \ - mv $$pyfile $(SHAREDIR) ; \ - ln -s ../../../share/$(DEBPKGNAME)/`basename $$pyfile` $(LIBDIR)/bin/`basename $$pyfile` ; \ - done - touch $(SHAREDIR)/spades_pipeline/__init__.py + #for pyfile in `ls $(LIBDIR)/bin/*.py` ; do \ + # mv $$pyfile $(SHAREDIR) ; \ + # ln -s ../../../share/$(DEBPKGNAME)/`basename $$pyfile` $(LIBDIR)/bin/`basename $$pyfile` ; \ + #done + #touch $(SHAREDIR)/spades_pipeline/__init__.py # install wrapper - cp -a debian/bin debian/$(DEBPKGNAME)/usr/ + #cp -a debian/bin debian/$(DEBPKGNAME)/usr/ # delete duplicate of license find debian -type f -name GPLv2.txt -delete find debian -type f -name LICENSE -delete @@ -35,11 +54,24 @@ # we just do not install it but rather remove the executable from # installation dir and replace it by a link to the Debian packaged bwa find debian -type f -name bwa-spades -delete + # sort out config files + #for cfile in `find debian/$(DEBPKGNAME)/etc -name "*.template"` ; do \ + # ifile=`echo $${cfile} | sed 's/\.template$$//'` ; \ + # if [ -e $${ifile} ] ; then \ + # rm -f $${cfile} ; \ + # else \ + # mv $${cfile} $${ifile} ; \ + # fi ; \ + #done + #find debian/$(DEBPKGNAME)/etc -name "*.i" -delete + #find debian/$(DEBPKGNAME)/etc -name "*.propertie" -delete + # remove config templates + #rm -rf debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)/configs override_dh_installdocs: dh_installdocs # move documentation - find debian/$(DEBPKGNAME)/usr -type f -name "*.html" -exec mv \{\} debian/$(DEBPKGNAME)/usr/share/doc/$(DEBPKGNAME) \; + #find debian/$(DEBPKGNAME)/usr -type f -name "*.html" -exec mv \{\} debian/$(DEBPKGNAME)/usr/share/doc/$(DEBPKGNAME) \; override_dh_installchangelogs: lynx -dump changelog.html > changelog _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit