[med-svn] r16721 - trunk/packages/wgs-assembler/trunk/debian

[Andreas Tille]

Author: tille
Date: 2014-04-17 13:54:42 +0000 (Thu, 17 Apr 2014)
New Revision: 16721

Modified:
   trunk/packages/wgs-assembler/trunk/debian/changelog
   trunk/packages/wgs-assembler/trunk/debian/control
   trunk/packages/wgs-assembler/trunk/debian/copyright
   trunk/packages/wgs-assembler/trunk/debian/rules
   trunk/packages/wgs-assembler/trunk/debian/watch
Log:
Drop code copy of samtools and use Debian packaged samtools instead (hopefully, not yet verified)


Modified: trunk/packages/wgs-assembler/trunk/debian/changelog
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/changelog	2014-04-17 13:33:58 UTC (rev 16720)
+++ trunk/packages/wgs-assembler/trunk/debian/changelog	2014-04-17 13:54:42 UTC (rev 16721)
@@ -1,8 +1,8 @@
-wgs-assembler (8.1-1) UNRELEASED; urgency=low
+wgs-assembler (8.1+dfsg-1) UNRELEASED; urgency=low
 
-  * TODO: does not build:
-          cd kmer/build ; ln -s ../Make.compilers . ; make makepath
-          /bin/sh: 1: cd: can't cd to kmer/build
+  Package builds at least if we drop the internal copy of samtools
+  It is not tested what side effects this might have (for instance
+  whether samtools functionality might be dropped at all)
 
   * Initial release (Closes: #395843)
 

Modified: trunk/packages/wgs-assembler/trunk/debian/control
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/control	2014-04-17 13:33:58 UTC (rev 16720)
+++ trunk/packages/wgs-assembler/trunk/debian/control	2014-04-17 13:54:42 UTC (rev 16721)
@@ -7,7 +7,8 @@
 Priority: optional
 Build-Depends: debhelper (>= 9),
                libbz2-dev,
-               zlib1g-dev
+               zlib1g-dev,
+               libbam-dev
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/wgs-assembler/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/wgs-assembler/trunk/

Modified: trunk/packages/wgs-assembler/trunk/debian/copyright
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/copyright	2014-04-17 13:33:58 UTC (rev 16720)
+++ trunk/packages/wgs-assembler/trunk/debian/copyright	2014-04-17 13:54:42 UTC (rev 16721)
@@ -2,6 +2,7 @@
 Upstream-Name: WGS-Assembler
 Upstream-Contact: Brian Walenz
 Source: http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/
+Files-Excluded: samtools*
 
 Files: *
 Copyright: © 2000-2011 M. K. N. Lawniczak, S. J. Emrich, A. K. Holloway,

Modified: trunk/packages/wgs-assembler/trunk/debian/rules
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/rules	2014-04-17 13:33:58 UTC (rev 16720)
+++ trunk/packages/wgs-assembler/trunk/debian/rules	2014-04-17 13:54:42 UTC (rev 16721)
@@ -19,7 +19,7 @@
 #	cd kmer; ln -sf Linux-* installdir
 
 	# do stuff for kmer
-	cd kmer && sh configure.sh && make install && ln -sf Linux-* installdir
+	cd kmer && sh configure.sh && SAMTOOLS=/usr/include/samtools make install && ln -sf Linux-* installdir
 	# do stuff for wgs-assembler
 	$(MAKE) -C src
 	ln -sf Linux-* installdir
@@ -38,5 +38,5 @@
 
 get-orig-source:
 	mkdir -p ../tarballs
-	uscan --verbose --force-download --destdir=../tarballs
+	uscan --verbose --force-download --repack --repack-compression bz2 --destdir=../tarballs
 

Modified: trunk/packages/wgs-assembler/trunk/debian/watch
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/watch	2014-04-17 13:33:58 UTC (rev 16720)
+++ trunk/packages/wgs-assembler/trunk/debian/watch	2014-04-17 13:54:42 UTC (rev 16721)
@@ -1,2 +1,3 @@
 version=3
-http://sf.net/wgs-assembler/wgs-([\d\.]+)\.tar\.bz2
+opts=dversionmangle=s/(\+dfsg)// \
+   http://sf.net/wgs-assembler/wgs-([\d\.]+)\.tar\.bz2