[med-svn] r12342 - in trunk/packages/sift/trunk/debian: . patches

[Laszlo Kajan]

Author: lkajan-guest
Date: 2012-10-08 16:29:06 +0000 (Mon, 08 Oct 2012)
New Revision: 12342

Added:
   trunk/packages/sift/trunk/debian/patches/jarfile
Modified:
   trunk/packages/sift/trunk/debian/
   trunk/packages/sift/trunk/debian/changelog
   trunk/packages/sift/trunk/debian/patches/ld-as-needed
   trunk/packages/sift/trunk/debian/patches/series
   trunk/packages/sift/trunk/debian/rules
Log:
merged changes from Ubuntu, fixed the .jar lintian warning, patched (unused) script to find .jar file in /usr/share


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

   + sift
*.substvars
files
*.debhelper.log


Modified: trunk/packages/sift/trunk/debian/changelog
===================================================================
--- trunk/packages/sift/trunk/debian/changelog	2012-10-08 15:34:46 UTC (rev 12341)
+++ trunk/packages/sift/trunk/debian/changelog	2012-10-08 16:29:06 UTC (rev 12342)
@@ -1,9 +1,21 @@
-sift (4.0.3b-4) UNRELEASED; urgency=low
+sift (4.0.3b-4) unstable; urgency=low
 
+  [ Andreas Tille ]
   * debian/upstream: Add citations
 
- -- Andreas Tille <tille at debian.org>  Fri, 25 May 2012 10:45:33 +0200
+  [ Laszlo Kajan ]
+  * Merge updates from Ubuntu 4.0.3b-3ubuntu1.
 
+ -- Laszlo Kajan <lkajan at rostlab.org>  Mon, 08 Oct 2012 16:41:15 +0200
+
+sift (4.0.3b-3ubuntu1) quantal; urgency=low
+
+  * Merge with Debian unstable. Remaining changes: 
+    - Update patches/debian/ld-as-needed:
+      Move libs from LDFLAGS to LIBS.
+
+ -- Michael Bienia <geser at ubuntu.com>  Sat, 26 May 2012 11:38:24 +0200
+
 sift (4.0.3b-3) unstable; urgency=low
 
   * Added patches from Michael Bienia <geser at ubuntu.com>.

Added: trunk/packages/sift/trunk/debian/patches/jarfile
===================================================================
--- trunk/packages/sift/trunk/debian/patches/jarfile	                        (rev 0)
+++ trunk/packages/sift/trunk/debian/patches/jarfile	2012-10-08 16:29:06 UTC (rev 12342)
@@ -0,0 +1,10 @@
+Author: Laszlo Kajan <lkajan at rostlab.org>
+Description: path to IntersectFeatures.jar
+ IntersectFeatures.jar file now in /usr/share, patch for calling script.
+--- a/bin/IntersectLocations.sh
++++ b/bin/IntersectLocations.sh
+@@ -1,3 +1,3 @@
+ #!/bin/sh
+-bin="/usr/local/projects/SIFT/sift4.0/bin/"
++bin="/usr/share/sift"
+ java -Xmx500m -jar $bin/IntersectFeatures.jar $1 $2 $3 $4 $5

Modified: trunk/packages/sift/trunk/debian/patches/ld-as-needed
===================================================================
--- trunk/packages/sift/trunk/debian/patches/ld-as-needed	2012-10-08 15:34:46 UTC (rev 12341)
+++ trunk/packages/sift/trunk/debian/patches/ld-as-needed	2012-10-08 16:29:06 UTC (rev 12342)
@@ -5,11 +5,14 @@
  use in CFLAGS and LDFLAGS.
  [Laszlo Kajan]
  Added dpkg-buildflags to CPPFLAGS.
+ Michael's explicit $(BIN) rule is made unnecessary by using LDLIBS instead
+ of his LIBS, as LDLIBS get used by the implicit make rules and achieves the
+ same result.
 Author: Michael Bienia <geser at ubuntu.com>
 Author: Laszlo Kajan <lkajan at rostlab.org>
 --- a/src/Makefile
 +++ b/src/Makefile
-@@ -9,8 +9,9 @@
+@@ -9,8 +9,10 @@
  	seqs_from_psiblast_res
  
  CC := gcc
@@ -17,7 +20,8 @@
 -LDFLAGS := -L$(lib-prefix)/lib -lblimps $(LDFLAGS)
 +CPPFLAGS := $(shell dpkg-buildflags --get CPPFLAGS)
 +CFLAGS := $(shell dpkg-buildflags --get CFLAGS) -Wno-unused-result -I$(include-prefix)/include/blimps -O2 -D__MAKE_PREFIX__=\"$(prefix)\"
-+LDFLAGS := $(shell dpkg-buildflags --get LDFLAGS) -L$(lib-prefix)/lib -lblimps -lm
++LDFLAGS := $(shell dpkg-buildflags --get LDFLAGS) -L$(lib-prefix)/lib
++LDLIBS := -lblimps -lm
  
  all: bin
  

Modified: trunk/packages/sift/trunk/debian/patches/series
===================================================================
--- trunk/packages/sift/trunk/debian/patches/series	2012-10-08 15:34:46 UTC (rev 12341)
+++ trunk/packages/sift/trunk/debian/patches/series	2012-10-08 16:29:06 UTC (rev 12342)
@@ -1,3 +1,4 @@
 fix_perl_interpreter_and_lib_path
 ld-as-needed
 fix_gcc_warnings
+jarfile

Modified: trunk/packages/sift/trunk/debian/rules
===================================================================
--- trunk/packages/sift/trunk/debian/rules	2012-10-08 15:34:46 UTC (rev 12341)
+++ trunk/packages/sift/trunk/debian/rules	2012-10-08 16:29:06 UTC (rev 12342)
@@ -1,11 +1,13 @@
 #!/usr/bin/make -f
 
 # Uncomment this to turn on verbose mode.
-export DH_VERBOSE=1
+#export DH_VERBOSE=1
 
-DESTDIR:=$(CURDIR)/debian/sift
+PACKAGE:=sift
+DESTDIR:=$(CURDIR)/debian/$(PACKAGE)
 VERSION:=4.0.3b
 prefix:=/usr
+pkgdatadir:=$(prefix)/share/$(PACKAGE)
 
 SIFT_BINDIR := $(prefix)/lib/sift/bin
 SIFT_SCRIPTDIR := $(prefix)/lib/sift/bin
@@ -46,7 +48,8 @@
 
 override_dh_install:
 	# lkajan: fastaseqs comes from the blimps package, this source does not have rules for creating it
-	dh_install -X.svn -X.swp -XManuals -Xfastaseqs -Xlinux -Xsolaris bin $(prefix)/lib/sift/
+	dh_install -X.svn -X.swp -XIntersectFeatures.jar -XManuals -Xfastaseqs -Xlinux -Xsolaris bin $(prefix)/lib/sift/
+	dh_install bin/IntersectFeatures.jar $(pkgdatadir)/
 	dh_install -X.svn -X.swp blimps/docs $(prefix)/share/sift/blimps/
 	#Links are created by debian/links
 	for f in SIFT_for_submitting_fasta_seq.csh SIFT_for_submitting_NCBI_gi_id.csh; do \
@@ -57,9 +60,12 @@
 	done;
 	chmod +x $(DESTDIR)$(prefix)/lib/sift/bin/perlscripts/separate_query_from_rest_of_seqs.pl
 	# look out: DNA_PROT_SUBROUTINES.pl is really a module (should be pm)!
-	for f in IntersectFeatures.jar SIFT_subroutines.pm DNA_PROT_SUBROUTINES.pl; do \
+	for f in SIFT_subroutines.pm DNA_PROT_SUBROUTINES.pl; do \
 		chmod -x $(DESTDIR)$(prefix)/lib/sift/bin/$$f; \
 	done;
+	for f in IntersectFeatures.jar; do \
+		chmod -x $(DESTDIR)$(pkgdatadir)/$$f; \
+	done;
 
 get-orig-source:
 	mkdir -p ../tarballs