[med-svn] r9749 - in trunk/packages/sift/trunk/debian: . patches

Wed Feb 22 10:46:20 UTC 2012

Author: lkajan-guest
Date: 2012-02-22 10:46:19 +0000 (Wed, 22 Feb 2012)
New Revision: 9749

Added:
   trunk/packages/sift/trunk/debian/patches/
   trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path
   trunk/packages/sift/trunk/debian/patches/series
   trunk/packages/sift/trunk/debian/watch
Modified:
   trunk/packages/sift/trunk/debian/
   trunk/packages/sift/trunk/debian/changelog
   trunk/packages/sift/trunk/debian/control
   trunk/packages/sift/trunk/debian/links
   trunk/packages/sift/trunk/debian/rules
Log:
Soons changes, Laszlo committing on behalf of him


Property changes on: trunk/packages/sift/trunk/debian
___________________________________________________________________
Added: svn:ignore
   + *.substvars
files
*.debhelper.log


Modified: trunk/packages/sift/trunk/debian/changelog
===================================================================

--- trunk/packages/sift/trunk/debian/changelog	2012-02-21 18:10:57 UTC (rev 9748)
+++ trunk/packages/sift/trunk/debian/changelog	2012-02-22 10:46:19 UTC (rev 9749)
@@ -1,3 +1,10 @@
+sift (4.0.3b-2) lucid; urgency=low
+
+  * Update to new upstream
+  * Re-hack build rules
+
+ -- H. Soon Gweon (Key for package building) <soonio at gmail.com>  Mon, 20 Feb 2012 18:01:12 +0000
+
 sift (3.0-1) UNRELEASED; urgency=low
 
   * Initial release (Closes: #????)

Modified: trunk/packages/sift/trunk/debian/control
===================================================================
--- trunk/packages/sift/trunk/debian/control	2012-02-21 18:10:57 UTC (rev 9748)
+++ trunk/packages/sift/trunk/debian/control	2012-02-22 10:46:19 UTC (rev 9749)
@@ -2,9 +2,10 @@
 Section: science
 Priority: extra
 Maintainer: Laszlo Kajan <lkajan at rostlab.org>
-Build-Depends: debhelper (>= 7)
+Uploaders: H. Soon Gweon <soonio at gmail.com>, Tim Booth <tbooth at ceh.ac.uk>
+Build-Depends: debhelper (>= 7), libblimps3-dev
 Standards-Version: 3.9.1
-Homepage: http://blocks.fhcrc.org/sift/SIFT_help.html
+Homepage: http://sift.jcvi.org
 
 Package: sift
 Architecture: any

Modified: trunk/packages/sift/trunk/debian/links
===================================================================
--- trunk/packages/sift/trunk/debian/links	2012-02-21 18:10:57 UTC (rev 9748)
+++ trunk/packages/sift/trunk/debian/links	2012-02-22 10:46:19 UTC (rev 9749)
@@ -1 +1,3 @@
-usr/bin/sift_for_submitting_fasta_seq.csh usr/bin/sift
+usr/lib/sift/bin/SIFT_exome_nssnvs.pl usr/bin/SIFT_exome_nssnvs.pl
+#usr/lib/sift/bin/sift_for_submitting_fasta_seq.csh usr/bin/sift
+#usr/lib/sift/bin/consensus_to_seq usr/bin/consensus_to_seq

Added: trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path
===================================================================
--- trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path	                        (rev 0)
+++ trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path	2012-02-22 10:46:19 UTC (rev 9749)
@@ -0,0 +1,31 @@
+--- a/bin/SIFT_exome_nssnvs.pl
++++ b/bin/SIFT_exome_nssnvs.pl
+@@ -1,4 +1,8 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
++
++#Location of all the SIFT grot on Debian.
++use lib '/usr/lib/sift/bin';
++
+ use List::Util qw[min max];
+ use File::Copy;
+ use Getopt::Std;
+--- a/bin/SIFT_exome_indels.pl
++++ b/bin/SIFT_exome_indels.pl
+@@ -1,4 +1,6 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
++
++use lib '/usr/lib/sift/bin';
+ 
+ # This program is licensed to you under the Fred
+ # Hutchinos Cancer Research Center (FHCRC)
+@@ -12,7 +14,7 @@
+ use Tie::IxHash;
+ use File::Copy;
+ use Getopt::Std;
+-$ENV{'SIFT_HOME'} = '/usr/local/projects/SIFT/sift4.0.1';
++$ENV{'SIFT_HOME'} = '/usr/share/sift';
+ $SIFT_HOME = $ENV{'SIFT_HOME'};
+ use vars qw($opt_i $opt_c $opt_d $opt_o);
+ getopts("i:c:d:o:");

Added: trunk/packages/sift/trunk/debian/patches/series
===================================================================
--- trunk/packages/sift/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/sift/trunk/debian/patches/series	2012-02-22 10:46:19 UTC (rev 9749)
@@ -0,0 +1 @@
+fix_perl_interpreter_and_lib_path

Modified: trunk/packages/sift/trunk/debian/rules
===================================================================
--- trunk/packages/sift/trunk/debian/rules	2012-02-21 18:10:57 UTC (rev 9748)
+++ trunk/packages/sift/trunk/debian/rules	2012-02-22 10:46:19 UTC (rev 9749)
@@ -9,83 +9,25 @@
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
+%:
+	dh --with quilt $@
 
+override_dh_auto_clean:
+	rm -rf bin/linux
+	rm -rf bin/solaris
+	( cd bin ; rm -f choose_seqs_via_psiblastseedmedian consensus_to_seq psiblast_res_to_fasta_dbpairwise \
+	clump_output_alignedseq fastaseqs info_on_seqs seqs_from_psiblast_res )
 
+override_dh_auto_build:
+	( cd src ; \
+	  for f in `grep '^\./cccb' compile.csh | cut -d ' ' -f 2` ; do \
+		gcc -O2 -o $$f $$f.c -lblimps -lm -I/usr/include/blimps ; \
+		mv $$f ../bin ; \
+	  done )
 
+override_dh_install:
+	dh_install -X.svn bin /usr/lib/sift/
+	#Below command simply replaced with -X above
+	#find debian/sift -type d -name '.svn' -prune -exec rm -rf '{}' ';'
+	#Links are created by debian/links
 
-configure: configure-stamp
-configure-stamp:
-	dh_testdir
-	# Add here commands to configure the package.
-
-	touch configure-stamp
-
-
-build: build-stamp
-
-build-stamp: configure-stamp  
-	dh_testdir
-
-	# Add here commands to compile the package.
-	$(MAKE) prefix=/usr
-	#docbook-to-man debian/sift.sgml > sift.1
-
-	touch $@
-
-clean: 
-	dh_testdir
-	dh_testroot
-	rm -f build-stamp configure-stamp
-
-	# Add here commands to clean up after the build process.
-	$(MAKE) prefix=/usr distclean
-
-	dh_clean 
-
-install: build
-	dh_testdir
-	dh_testroot
-	dh_prep
-	dh_installdirs
-
-	# Add here commands to install the package into debian/sift.
-	$(MAKE) DESTDIR=$(CURDIR)/debian/sift prefix=/usr install
-
-
-# Build architecture-independent files here.
-binary-indep: build install
-# We have nothing to do by default.
-
-# Build architecture-dependent files here.
-binary-arch: build install
-	dh_testdir
-	dh_testroot
-	dh_installchangelogs ChangeLog
-	dh_installdocs
-	dh_installexamples
-#	dh_install
-#	dh_installmenu
-#	dh_installdebconf	
-#	dh_installlogrotate
-#	dh_installemacsen
-#	dh_installpam
-#	dh_installmime
-#	dh_python
-#	dh_installinit
-#	dh_installcron
-#	dh_installinfo
-	dh_installman
-	dh_link
-	dh_strip
-	dh_compress
-	dh_fixperms
-#	dh_perl
-#	dh_makeshlibs
-	dh_installdeb
-	dh_shlibdeps
-	dh_gencontrol
-	dh_md5sums
-	dh_builddeb
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure

Added: trunk/packages/sift/trunk/debian/watch
===================================================================
--- trunk/packages/sift/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/sift/trunk/debian/watch	2012-02-22 10:46:19 UTC (rev 9749)
@@ -0,0 +1,6 @@
+version=3
+# This is a variant HTTP format which allows direct specification of
+# the homepage:
+# Homepage  Pattern  [Version  [Action]]
+http://sift.jcvi.org \
+	www/sift([0-9][0-9a-z.]*)\.tar\.[gzbl2]{2,3}


