[med-svn] [grinder] 01/01: Deal wiht modules moved to BioLinux

[Andreas Tille]

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tille pushed a commit to branch master
in repository grinder.

commit 652324fb291b290c069da1a596bcfdfdd00a3d9b
Author: Andreas Tille <tille at debian.org>
Date:   Fri Sep 13 09:08:05 2013 +0200

    Deal wiht modules moved to BioLinux
---
 debian/changelog |   12 ++++++++++++
 debian/rules     |   14 +++++++++++---
 2 files changed, 23 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 71bef53..a883455 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,15 @@
+grinder (0.5.3-3) UNRELEASED; urgency=low
+
+  * debian/rules:
+     - Move more duplicates from libbio-perl-perl out of the way
+       Closes: #722650
+       Remark: It seems libbio-perl-perl is integrating actively code
+       from grinder and includes it into their distribution.  Finally
+       now are all modules from the Bio directory integrated into
+       BioPerl.
+
+ -- Andreas Tille <tille at debian.org>  Fri, 13 Sep 2013 08:25:06 +0200
+
 grinder (0.5.3-2) unstable; urgency=low
 
   * debian/rules:
diff --git a/debian/rules b/debian/rules
index e829529..7972eb6 100755
--- a/debian/rules
+++ b/debian/rules
@@ -37,20 +37,28 @@ MOREFILE = $(MANDIR)/more.$(SECTION)
 	dh $@
 
 override_dh_auto_configure:
-	# some files are duplicates from BioPerl and create conflicts when trying
-	# to install the package.  So the are moved out of the way in the beginning
-	# and droped into place in the clean target again
+	# It seems libbio-perl-perl is integrating actively code
+	# from grinder and includes it into their distribution.  Finally
+	# now are all modules from the Bio directory integrated into
+	# BioPerl.  The single file moving was kept just for the reason
+	# to have some template once a new Grinder version might come up
+	# with new code
 	mkdir -p _disposal/Bio
 	# MYMETA.yml will be changed and not reverted in clean target - use the chance to conserve it here
 	cp -a MYMETA.yml _disposal
 	mv lib/Bio/PrimarySeq*.pm		_disposal/Bio
 	mkdir -p _disposal/Bio/DB
 	mv lib/Bio/DB/Fasta.pm			_disposal/Bio/DB
+	mv lib/Bio/DB/IndexedBase.pm		_disposal/Bio/DB
 	mkdir -p _disposal/Bio/Seq
 	mv lib/Bio/Seq/SeqFastaSpeedFactory.pm	_disposal/Bio/Seq
+	mv lib/Bio/Seq/SimulatedRead.pm		_disposal/Bio/Seq
 	mkdir -p _disposal/Bio/SeqFeature
+	mv lib/Bio/SeqFeature/Amplicon.pm	_disposal/Bio/SeqFeature
 	mv lib/Bio/SeqFeature/Primer.pm		_disposal/Bio/SeqFeature
+	mv lib/Bio/SeqFeature/SubSeq.pm		_disposal/Bio/SeqFeature
 	mkdir -p _disposal/Bio/Tools
+	mv lib/Bio/Tools/AmpliconSearch.pm	_disposal/Bio/Tools
 	mv lib/Bio/Tools/IUPAC.pm		_disposal/Bio/Tools
 	dh_auto_configure
 

-- 
Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/grinder.git