[med-svn] r6157 - trunk/packages/wgs-assembler/trunk/debian

[Steffen Möller]

Author: moeller
Date: 2011-03-03 14:20:41 +0000 (Thu, 03 Mar 2011)
New Revision: 6157

Added:
   trunk/packages/wgs-assembler/trunk/debian/wgs-assembler.dirs
Removed:
   trunk/packages/wgs-assembler/trunk/debian/README.source
Modified:
   trunk/packages/wgs-assembler/trunk/debian/
   trunk/packages/wgs-assembler/trunk/debian/README.Debian
   trunk/packages/wgs-assembler/trunk/debian/control
   trunk/packages/wgs-assembler/trunk/debian/rules
   trunk/packages/wgs-assembler/trunk/debian/watch
Log:
Builds for me.



Property changes on: trunk/packages/wgs-assembler/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
   + 1

Modified: trunk/packages/wgs-assembler/trunk/debian/README.Debian
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/README.Debian	2011-03-03 13:37:08 UTC (rev 6156)
+++ trunk/packages/wgs-assembler/trunk/debian/README.Debian	2011-03-03 14:20:41 UTC (rev 6157)
@@ -1,6 +1,14 @@
 wgs-assembler for Debian
 ------------------------
 
-<possible notes regarding this package - if none, delete this file>
+This package is still worked on. To do:
 
- -- root <whs at eaglegenomics.com>  Sat, 29 Jan 2011 16:40:00 +0000
+ * watch file does not yet allow downloads
+ * kmer should become a binary on its own
+
+Upstream could need some help with shared libraries, and possibly
+also with other things. While gaining experience with it all,
+the package shall reside in the experimental section as a start.
+
+ -- William Spooner <whs at eaglegenomics.com>  Sat, 29 Jan 2011 16:40:00 +0000
+    Steffen Moeller <moeller at debian.org>

Deleted: trunk/packages/wgs-assembler/trunk/debian/README.source
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/README.source	2011-03-03 13:37:08 UTC (rev 6156)
+++ trunk/packages/wgs-assembler/trunk/debian/README.source	2011-03-03 14:20:41 UTC (rev 6157)
@@ -1,9 +0,0 @@
-wgs-assembler for Debian
-------------------------
-
-<this file describes information about the source package, see Debian policy
-manual section 4.14. You WILL either need to modify or delete this file>
-
-
-
-

Modified: trunk/packages/wgs-assembler/trunk/debian/control
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/control	2011-03-03 13:37:08 UTC (rev 6156)
+++ trunk/packages/wgs-assembler/trunk/debian/control	2011-03-03 14:20:41 UTC (rev 6157)
@@ -13,6 +13,11 @@
 Package: wgs-assembler
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: Genome DNA sequence assembler
- Genome DNA assembler originally developed by Celera, but since open-sourced
- and extended to provide hybrid assemblies across an expanding number of sequence types.
+Description: Whole-Genome DNA sequence assembler
+ WGS stands for 'whole genome shotgun' and refers to the concept
+ to perform an assembly of large genomes from many smallish random
+ reads.
+ .
+ The assembler was originally developed by Celera and is of strong
+ historic value. I was open-sourced and since extended to provide
+ hybrid assemblies across an expanding number of sequence types.

Modified: trunk/packages/wgs-assembler/trunk/debian/rules
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/rules	2011-03-03 13:37:08 UTC (rev 6156)
+++ trunk/packages/wgs-assembler/trunk/debian/rules	2011-03-03 14:20:41 UTC (rev 6157)
@@ -13,11 +13,22 @@
 	dh $@ 
 
 override_dh_auto_build:
+	export PATH=$$PATH:. ; \
+	cd kmer/build ; \
+	ln -s ../Make.compilers . ; \
+	make makepath
 	cd kmer; \
-	ln -s build/makepath.pl makepath ; \
+	ln -sf build/makepath.pl build/makepath . ; \
 	sh configure.sh; \
-	gmake install; \
-	cd ../src; \
-	gmake; \
-	cd ..
+	make install
+	ln -s kmer/Linux-* kmer/installdir
+	$(MAKE) -C src
+	ln -s Linux-* installdir
 
+override_dh_install:
+	cp installdir/bin/* $(CURDIR)/debian/wgs-assembler/usr/bin/
+	cp kmer/installdir/bin/* $(CURDIR)/debian/wgs-assembler/usr/bin/
+	cp kmer/installdir/include/* $(CURDIR)/debian/wgs-assembler/usr/include/kmer/
+
+clean::
+	rm -rf kmer/makepath.pl kmer/installdir kmer/build/Make.compilers installdir

Modified: trunk/packages/wgs-assembler/trunk/debian/watch
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/watch	2011-03-03 13:37:08 UTC (rev 6156)
+++ trunk/packages/wgs-assembler/trunk/debian/watch	2011-03-03 14:20:41 UTC (rev 6157)
@@ -1,2 +1,2 @@
 version=3
-http://sf.net/wgs-assembler/wgs-([\d\.]+)\.tar\.bz2
+http://sf.net/wgs-assembler/wgs-([\d\.]+)\.tar\.bz

Added: trunk/packages/wgs-assembler/trunk/debian/wgs-assembler.dirs
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/wgs-assembler.dirs	                        (rev 0)
+++ trunk/packages/wgs-assembler/trunk/debian/wgs-assembler.dirs	2011-03-03 14:20:41 UTC (rev 6157)
@@ -0,0 +1,2 @@
+usr/include/kmer
+usr/bin