[med-svn] [SCM] grinder branch, master, updated. upstream/0.5.3-15-gf5f2849

[Andreas Tille]

The following commit has been merged in the master branch:
commit f5f28497ca25c5bbbd4e98285a95804b60bb8937
Author: Andreas Tille <tille at debian.org>
Date:   Thu Aug 1 11:44:24 2013 +0200

    Move some files duplicated from bioperl out of the way in configure step and restore them in clean target
    
    Note: Any more elegant solution to prevent installation of duplicated files would be welcome.

diff --git a/debian/changelog b/debian/changelog
index c4c7046..d79dbd7 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,10 @@
 grinder (0.5.3-2) UNRELEASED; urgency=low
 
-  * debian/rules: clean target should recreate original tarball
+  * debian/rules:
+     - clean target should recreate original tarball
+     - Move some files duplicated from bioperl out of the way in
+       configure step and restore them in clean target
+       Closes: #718407
 
  -- Andreas Tille <tille at debian.org>  Thu, 01 Aug 2013 11:05:04 +0200
 
diff --git a/debian/rules b/debian/rules
index 1e8f14c..e829529 100755
--- a/debian/rules
+++ b/debian/rules
@@ -36,6 +36,24 @@ 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
+	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
+	mkdir -p _disposal/Bio/Seq
+	mv lib/Bio/Seq/SeqFastaSpeedFactory.pm	_disposal/Bio/Seq
+	mkdir -p _disposal/Bio/SeqFeature
+	mv lib/Bio/SeqFeature/Primer.pm		_disposal/Bio/SeqFeature
+	mkdir -p _disposal/Bio/Tools
+	mv lib/Bio/Tools/IUPAC.pm		_disposal/Bio/Tools
+	dh_auto_configure
+
 # Because of Grinder's random output, some tests are brittle and may fail...
 # Only test that the program loads successfully
 override_dh_auto_test:
@@ -54,3 +72,10 @@ override_dh_auto_build:
 override_dh_auto_clean:
 	dh_auto_clean
 	rm -rf $(MANDIR)
+	if [ -d _disposal ] ; then \
+	    if [ -e _disposal/MYMETA.yml ] ; then mv _disposal/MYMETA.yml . ; fi ; \
+	    for pm in `cd _disposal ; find Bio -type f ; cd ..` ; do \
+		mv _disposal/$${pm} lib/$${pm} ; \
+	    done ; \
+	fi
+	rm -rf _disposal

-- 
Versatile shotgun and amplicon read simulator