The following commit has been merged in the master branch:
commit f5f28497ca25c5bbbd4e98285a95804b60bb8937
Author: Andreas Tille <[email protected]>
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 <[email protected]> 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
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