[med-svn] r7694 - trunk/packages/seqan/trunk/debian

[Charles Plessy]

Author: plessy
Date: 2011-09-07 04:46:01 +0000 (Wed, 07 Sep 2011)
New Revision: 7694

Modified:
   trunk/packages/seqan/trunk/debian/control
   trunk/packages/seqan/trunk/debian/rules
Log:
Build according to upstream's instructions, and avoid programs with generic names in /usr/bin.

 - Build applications using Cmake
 - place them in /usr/lib/seqan/bin
 - provide /usr/bin links for applications already distributed in sequan_1.2-1 package.

Unfortunately, this trigers an error reported by Lintian: binary-or-shlib-defines-rpath
(To be investigated).

See also:

 - http://bugs.debian.org/640763#20
 - http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/GettingStarted?version=27


Modified: trunk/packages/seqan/trunk/debian/control
===================================================================
--- trunk/packages/seqan/trunk/debian/control	2011-09-07 00:24:50 UTC (rev 7693)
+++ trunk/packages/seqan/trunk/debian/control	2011-09-07 04:46:01 UTC (rev 7694)
@@ -4,7 +4,7 @@
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Soeren Sonnenburg <sonne at debian.org>,
  Andreas Tille <tille at debian.org>
-Build-Depends: cdbs, debhelper (>= 7)
+Build-Depends: cdbs, debhelper (>= 7), cmake
 Standards-Version: 3.9.1
 Homepage: http://www.seqan.de/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/seqan/

Modified: trunk/packages/seqan/trunk/debian/rules
===================================================================
--- trunk/packages/seqan/trunk/debian/rules	2011-09-07 00:24:50 UTC (rev 7693)
+++ trunk/packages/seqan/trunk/debian/rules	2011-09-07 04:46:01 UTC (rev 7694)
@@ -4,27 +4,23 @@
 
 build/seqan-apps:: debian/stamp-build-seqan-apps
 debian/stamp-build-seqan-apps:
-	( cd $(CURDIR)/apps && make )
+	( cd $(CURDIR)/cmake && cmake . && make VERBOSE=1)
 	touch $@
 
 install/seqan-apps:: debian/stamp-install-seqan-apps
 debian/stamp-install-seqan-apps:
 	mkdir -p $(CURDIR)/debian/seqan-apps/usr/bin
+	mkdir -p $(CURDIR)/debian/seqan-apps/usr/lib/sequan/bin
 	mkdir -p $(CURDIR)/debian/seqan-apps/usr/share/doc/seqan-apps
 	#install binaries
-	cp -p $(CURDIR)/apps/dfi/dfi $(CURDIR)/debian/seqan-apps/usr/bin/
-	cp -p $(CURDIR)/apps/micro_razers/micro_razers $(CURDIR)/debian/seqan-apps/usr/bin/
-	cp -p $(CURDIR)/apps/pair_align/pair_align $(CURDIR)/debian/seqan-apps/usr/bin/
-	cp -p $(CURDIR)/apps/razers/razers $(CURDIR)/debian/seqan-apps/usr/bin/
-	cp -p $(CURDIR)/apps/seqan_tcoffee/seqan_tcoffee $(CURDIR)/debian/seqan-apps/usr/bin/
-	cp -p $(CURDIR)/apps/seqcons/seqcons $(CURDIR)/debian/seqan-apps/usr/bin/
-	cp -p $(CURDIR)/apps/tree_recon/tree_recon $(CURDIR)/debian/seqan-apps/usr/bin/
+	for APP in dfi insegt mason micro_razers pair_align param_chooser rabema razers razers2 read_analyzer rep_sep sak seqan_tcoffee seqcons snp_store splazers stellar tree_recon ; do \
+	  cp -p $(CURDIR)/cmake/apps/$$APP $(CURDIR)/debian/seqan-apps/usr/lib/sequan/bin/ ; done
+	# Links for compatibility with seqan 1.2-1
+	for APP in dfi micro_razers pair_align razers seqan_tcoffee seqcons tree_recon ; do \
+	  ln -s /usr/lib/sequan/bin/$$APP $(CURDIR)/debian/seqan-apps/usr/bin/$$APP ; done
 	#install readmes
-	cp -p $(CURDIR)/apps/dfi/README $(CURDIR)/debian/seqan-apps/usr/share/doc/seqan-apps/README.dfi
-	cp -p $(CURDIR)/apps/micro_razers/README $(CURDIR)/debian/seqan-apps/usr/share/doc/seqan-apps/README.micro_razers
-	cp -p $(CURDIR)/apps/razers/README $(CURDIR)/debian/seqan-apps/usr/share/doc/seqan-apps/README.razers
-	cp -p $(CURDIR)/apps/seqan_tcoffee/README $(CURDIR)/debian/seqan-apps/usr/share/doc/seqan-apps/README.seqan_tcoffee
-
+	for APP in dfi insegt mason micro_razers razers razers2 sak seqan_tcoffee splazers stellar ; do \
+	  cp -p $(CURDIR)/apps/$$APP/README $(CURDIR)/debian/seqan-apps/usr/share/doc/seqan-apps/README.$$APP ; done
 	touch $@
 
 install/seqan-dev:: debian/stamp-install-seqan-dev