[med-svn] [Git][med-team/spades4unicycler][master] 4 commits: Remove __pycache__ dirs

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / spades4unicycler


Commits:
10a2e3ca by Andreas Tille at 2021-12-14T13:59:27+01:00
Remove __pycache__ dirs

- - - - -
14612406 by Andreas Tille at 2021-12-14T15:21:50+01:00
Work into direction co-installation of spades and spades4unicycle

- - - - -
6acb9a9f by Andreas Tille at 2021-12-16T18:51:37+01:00
Work in direction of co-installability with spades

- - - - -
9e056a83 by Andreas Tille at 2021-12-16T18:52:10+01:00
Drop unneeded Files entry

- - - - -


6 changed files:

- debian/bin/spades → debian/bin/spades4unicycle
- debian/copyright
- debian/links
- debian/patches/0103_use-debian-packaged-bwa.patch
- debian/patches/adapt_to_debian_pathes.patch
- debian/rules


Changes:

=====================================
debian/bin/spades → debian/bin/spades4unicycle
=====================================
@@ -1,6 +1,6 @@
 #!/bin/sh
-SPADESDIR=/usr/lib/spades/bin
-SPADESSHARE=/usr/share/spades
+SPADESDIR=/usr/lib/spades4unicycler/bin
+SPADESSHARE=/usr/share/spades4unicycler
 exename=`basename $0`
 PATH=$SPADESDIR:$PATH
 if [ -f $SPADESDIR/${exename}.py ]; then


=====================================
debian/copyright
=====================================
@@ -162,7 +162,6 @@ Copyright: (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stro
 License: Expat
 
 Files: ext/include/kseq/*
-       ext/src/samtools/bcftools/kmin.*
 Copyright: (c) 2008-2011 Attractive Chaos <attractor at live.co.uk>
 License: Expat
 


=====================================
debian/links
=====================================
@@ -8,7 +8,7 @@ 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/spades-bwa
+usr/bin/bwa     usr/lib/spades4unicycler/bin/spades-bwa
 usr/share/man/man1/spades.1.gz /usr/share/man/man1/spades.py.1.gz
 usr/share/man/man1/truspades.1.gz /usr/share/man/man1/truspades.py.1.gz
 usr/share/man/man1/metaspades.1.gz /usr/share/man/man1/metaspades.py.1.gz


=====================================
debian/patches/0103_use-debian-packaged-bwa.patch
=====================================
@@ -10,7 +10,7 @@ Description: SPAdes originally contained a code copy of bwa since the version
  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
+    ln -s /usr/bin/bwa /usr/lib/spades4unicycler/bin/bwa-spades
  which enables successful run of the test suite
 
 --- a/ext/tools/CMakeLists.txt


=====================================
debian/patches/adapt_to_debian_pathes.patch
=====================================
@@ -10,7 +10,7 @@ Description: There is no point in installing the Python modules under .../src
  spades_home = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
 -bin_home = os.path.join(spades_home, 'bin')
 -python_modules_home = os.path.join(spades_home, 'src')
-+bin_home = os.path.join('/usr/lib/spades', 'bin')
++bin_home = os.path.join('/usr/lib/spades4unicycler', 'bin')
 +python_modules_home = spades_home
  ext_python_modules_home = os.path.join(spades_home, 'ext', 'src', 'python_libs')
  spades_version = ''


=====================================
debian/rules
=====================================
@@ -9,7 +9,7 @@ CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS)
 CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) $(CPPFLAGS)
 LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
 TMPDIR     := $(CURDIR)/install_spades
-LIBDIR     := debian/$(DEB_SOURCE)/usr/lib/spades
+LIBDIR     := debian/$(DEB_SOURCE)/usr/lib/spades4unicycler
 mandir     := $(CURDIR)/debian/man
 debfolder  := $(CURDIR)/debian
 
@@ -21,7 +21,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 export LC_ALL = C
 
 %:
-	dh $@  --with python2 --sourcedirectory=src --buildsystem=cmake
+	dh $@  --with python3 --sourcedirectory=src --buildsystem=cmake
 
 override_dh_clean:
 	dh_clean -X.orig
@@ -76,21 +76,22 @@ override_dh_auto_install:
 
 override_dh_install:
 	dh_install
+	mv debian/$(DEB_SOURCE)/usr/share/spades debian/$(DEB_SOURCE)/usr/share/spades4unicycler
 	mkdir -p $(LIBDIR)
 	mv debian/$(DEB_SOURCE)/usr/bin $(LIBDIR)
 	mkdir -p debian/$(DEB_SOURCE)/usr/bin
-	install debian/bin/spades debian/$(DEB_SOURCE)/usr/bin/
-	chmod +x debian/$(DEB_SOURCE)/usr/bin/spades
-	rm -f debian/$(DEB_SOURCE)/usr/share/spades/GPLv2.txt
-	rm -f debian/$(DEB_SOURCE)/usr/share/spades/README.md
-	rm -f debian/$(DEB_SOURCE)/usr/share/spades/LICENSE
-	ln -s ../../../share/spades/VERSION debian/$(DEB_SOURCE)/usr/lib/spades/bin/VERSION
-
+	install debian/bin/spades* debian/$(DEB_SOURCE)/usr/bin/
+	chmod +x debian/$(DEB_SOURCE)/usr/bin/spades*
+	rm -f debian/$(DEB_SOURCE)/usr/share/spades4unicycler/GPLv2.txt
+	rm -f debian/$(DEB_SOURCE)/usr/share/spades4unicycler/README.md
+	rm -f debian/$(DEB_SOURCE)/usr/share/spades4unicycler/LICENSE
+	ln -s ../../../share/spades4unicycler/VERSION debian/$(DEB_SOURCE)/usr/lib/spades4unicycler/bin/VERSION
+	find debian -name __pycache__ | xargs rm -rf
 
 override_dh_installdocs:
 	dh_installdocs
-	rm -f debian/$(DEB_SOURCE)/usr/share/spades/*.html
-	rm -f debian/$(DEB_SOURCE)/usr/share/spades/manual.md
+	rm -f debian/$(DEB_SOURCE)/usr/share/spades4unicycler/*.html
+	rm -f debian/$(DEB_SOURCE)/usr/share/spades4unicycler/manual.md
 
 override_dh_installchangelogs:
 	LANG="C" LANGUAGE="en_US:en" LC_ALL=C.UTF-8 lynx -dump changelog.html > changelog



View it on GitLab: https://salsa.debian.org/med-team/spades4unicycler/-/compare/063ca224c7ef98598454c10bbebd98fe70f57aa0...9e056a839cbf2d63311a306c7c1b343b4b2e2daa

-- 
View it on GitLab: https://salsa.debian.org/med-team/spades4unicycler/-/compare/063ca224c7ef98598454c10bbebd98fe70f57aa0...9e056a839cbf2d63311a306c7c1b343b4b2e2daa
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