[med-svn] [Git][med-team/spades][master] 12 commits: Create symlink to VERSION file in the place where spades is looking for it
Alexandre Mestiashvili
gitlab at salsa.debian.org
Mon Sep 10 17:23:54 BST 2018
Alexandre Mestiashvili pushed to branch master at Debian Med / spades
Commits:
c9ac2dcb by Alexandre Mestiashvili at 2018-09-10T09:37:25Z
Create symlink to VERSION file in the place where spades is looking for it
- - - - -
3beaf190 by Alexandre Mestiashvili at 2018-09-10T09:39:46Z
Update PYTHONPATH for spades wrapper
- - - - -
e2164b15 by Alexandre Mestiashvili at 2018-09-10T13:19:53Z
Update d/rules, fix VERSION location for tests
- - - - -
c1d849a6 by Alexandre Mestiashvili at 2018-09-10T13:33:16Z
Inject PYTHONPATH for tests
- - - - -
55215be0 by Alexandre Mestiashvili at 2018-09-10T13:34:07Z
qilt delete 0113_adjust_paths.patch
- - - - -
c86d1416 by Alexandre Mestiashvili at 2018-09-10T13:38:23Z
Tests depend on bwa
- - - - -
10a8ed70 by Alexandre Mestiashvili at 2018-09-10T13:47:13Z
Add tmp link for tests for bwa-spades
- - - - -
e6badf39 by Alexandre Mestiashvili at 2018-09-10T14:07:15Z
Spades expects spades-bwa binary, not bwa-spades
- - - - -
22ae72c5 by Alexandre Mestiashvili at 2018-09-10T14:12:50Z
Remove *.pyc files
- - - - -
2ee54ae9 by Alexandre Mestiashvili at 2018-09-10T15:29:27Z
Add patch 0118_adjust_spades_home_again.patch replacing 0113_adjust_paths.patch
- - - - -
eec57b9e by Alexandre Mestiashvili at 2018-09-10T16:05:42Z
Update override_dh_auto_test: link to data/VERSION files
- - - - -
d4bd1d89 by Alexandre Mestiashvili at 2018-09-10T16:19:09Z
Drop PYTHONPATH from wrapper and dh_auto_tests
not needed With correct spades_init.py
- - - - -
6 changed files:
- debian/bin/spades
- debian/links
- + debian/patches/0118_adjust_spades_home_again.patch
- debian/patches/series
- debian/rules
- debian/tests/control
Changes:
=====================================
debian/bin/spades
=====================================
@@ -1,6 +1,6 @@
#!/bin/sh
SPADESDIR=/usr/lib/spades/bin
-# SPADESSHARE=/usr/share/spades
+SPADESSHARE=/usr/share/spades
exename=`basename $0`
PATH=$SPADESDIR:$PATH
if [ -f $SPADESDIR/${exename}.py ]; then
=====================================
debian/links
=====================================
@@ -10,7 +10,7 @@ usr/bin/spades usr/bin/plasmidspades.py
usr/bin/spades usr/bin/plasmidspades
usr/bin/spades usr/bin/rnaspades.py
usr/bin/spades usr/bin/rnaspades
-usr/bin/bwa usr/lib/spades/bin/bwa-spades
+usr/bin/bwa usr/lib/spades/bin/spades-bwa
usr/share/man/man1/spades.1.gz /usr/share/man/man1/spades.py.1.gz
usr/share/man/man1/dipspades.1.gz /usr/share/man/man1/dipspades.py.1.gz
usr/share/man/man1/truspades.1.gz /usr/share/man/man1/truspades.py.1.gz
=====================================
debian/patches/0118_adjust_spades_home_again.patch
=====================================
@@ -0,0 +1,11 @@
+--- spades.orig/spades_init.py
++++ spades/spades_init.py
+@@ -32,7 +32,7 @@
+ if isfile(os.path.join(spades_home, 'spades-core')):
+ install_prefix = dirname(spades_home)
+ bin_home = join(install_prefix, 'bin')
+- spades_home = join(install_prefix, 'share', 'spades')
++ spades_home = join(install_prefix, '../../', 'share', 'spades')
+ python_modules_home = spades_home
+ ext_python_modules_home = spades_home
+
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+0118_adjust_spades_home_again.patch
0002_use_debian_packaged_python-joblib.patch
0003_accept-system-bwa.patch
0101_cmake_ignore_removed_python-yaml.patch
@@ -10,7 +11,6 @@
# use-debian-packaged-bamtools.patch ## <<-- does not work - see patch description
# use-debian-packaged-yaml-cpp.patch ## <<-- does not work - see patch description
0110_build_single_thread.patch
-0113_adjust_paths.patch
0114_use_debian_provided_libs.patch
0115_enable_compiler_messages.patch
0111_use_full_config_dirs.patch
=====================================
debian/rules
=====================================
@@ -54,6 +54,10 @@ override_dh_installman:
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ # Ugly hack to make files available for dh_aut_test and autopkgtest
+ mkdir -p $(CURDIR)/../share/
+ ln -s $(CURDIR)/install_spades/share/spades $(CURDIR)/../share/
+ ln -s /usr/bin/bwa $(CURDIR)/install_spades/bin/spades-bwa
$(TMPDIR)/bin/spades.py --test
$(TMPDIR)/bin/dipspades.py --test
$(TMPDIR)/bin/metaspades.py --test
@@ -62,10 +66,14 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
# is still not in the right place. Let's do this later in an
# autopkgtest.
# $(TMPDIR)/bin/truspades.py --test
+ # Cleunup symlinks
+ rm -rf $(CURDIR)/../share/
+ unlink $(CURDIR)/install_spades/bin/spades-bwa
endif
override_dh_auto_install:
echo "Nothing to install"
+ find $(CURDIR) -name *.pyc -delete
override_dh_install:
dh_install
@@ -76,6 +84,7 @@ override_dh_install:
chmod +x debian/$(DEB_SOURCE)/usr/bin/spades
rm -f debian/$(DEB_SOURCE)/usr/share/spades/GPLv2.txt
rm -f debian/$(DEB_SOURCE)/usr/share/spades/LICENSE
+ ln -s ../../../share/spades/VERSION debian/$(DEB_SOURCE)/usr/lib/spades/bin/VERSION
override_dh_installdocs:
dh_installdocs
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
-Tests: run-upstreams-tests
-Depends: @
+Tests: run-upstreams-tests
+Depends: @,bwa
Restrictions: allow-stderr
View it on GitLab: https://salsa.debian.org/med-team/spades/compare/3e6039eac2ea4b977d2e53ce09313628853f03fe...d4bd1d8988a60b6e9129b98133b436534be3f0a7
--
View it on GitLab: https://salsa.debian.org/med-team/spades/compare/3e6039eac2ea4b977d2e53ce09313628853f03fe...d4bd1d8988a60b6e9129b98133b436534be3f0a7
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