[med-svn] r18903 - in trunk/packages/spades/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Wed Mar 4 13:12:02 UTC 2015
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.support at 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: pulkkins at gmail.com
-License: GPLv3+
-Comment: This is a code copy from
- http://code.google.com/p/otkpp/
-
Files: debian/*
Copyright: 2014 Andreas Tille <tille at 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 <tille at 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
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