[med-svn] [grinder] 06/07: Adapt packaging to new upstream version

[Andreas Tille]

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tille pushed a commit to branch master
in repository grinder.

commit b89ab91efb4bf645fdfa807815305ca23626b570
Author: Andreas Tille <tille at debian.org>
Date:   Sun Jan 24 10:14:34 2016 +0100

    Adapt packaging to new upstream version
---
 debian/changelog |  2 +-
 debian/rules     | 23 +----------------------
 2 files changed, 2 insertions(+), 23 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 7a07d6f..fa04876 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,6 @@
 grinder (0.5.4-1) UNRELEASED; urgency=medium
 
-  * New upstream version
+  * New upstream version (parts of BioPerl are not part of Grinder any more)
   * cme fix dpkg-control
 
  -- Andreas Tille <tille at debian.org>  Sun, 24 Jan 2016 09:53:03 +0100
diff --git a/debian/rules b/debian/rules
index b8bc7d1..e587e99 100755
--- a/debian/rules
+++ b/debian/rules
@@ -7,7 +7,7 @@ SECTION := 1
 MANDIR  := debian/man
 
 NAME1   = $(PACKAGE)
-SCRIPT1 = script/$(NAME1)
+SCRIPT1 = bin/$(NAME1)
 DESC1   = 'Versatile omics shotgun and amplicon sequencing read simulator'
 MAN1    = $(MANDIR)/$(NAME1).$(SECTION)
 
@@ -37,29 +37,8 @@ MOREFILE = $(MANDIR)/more.$(SECTION)
 	dh $@
 
 override_dh_auto_configure:
-	# 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
 
 # Because of Grinder's random output, some tests are brittle and may fail...

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