[med-svn] r16756 - in trunk/packages/wgs-assembler/trunk/debian: . bin patches
Andreas Tille
tille at moszumanska.debian.org
Wed Apr 23 13:03:26 UTC 2014
Author: tille
Date: 2014-04-23 13:03:24 +0000 (Wed, 23 Apr 2014)
New Revision: 16756
Added:
trunk/packages/wgs-assembler/trunk/debian/bin/
trunk/packages/wgs-assembler/trunk/debian/bin/runCA
trunk/packages/wgs-assembler/trunk/debian/libwgs-kmer-dev.install
trunk/packages/wgs-assembler/trunk/debian/wgs-assembler.install
trunk/packages/wgs-assembler/trunk/debian/wgs-kmer.install
Removed:
trunk/packages/wgs-assembler/trunk/debian/wgs-assembler.dirs
Modified:
trunk/packages/wgs-assembler/trunk/debian/control
trunk/packages/wgs-assembler/trunk/debian/patches/format-security.patch
trunk/packages/wgs-assembler/trunk/debian/rules
Log:
Several packaging enhancements: working clean target, move single modules to /usr/lib/wgs-assembler and drop only runCA in /usr/bin, fixing interpreter PATH, libwgs-kmer-dev package
Added: trunk/packages/wgs-assembler/trunk/debian/bin/runCA
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/bin/runCA (rev 0)
+++ trunk/packages/wgs-assembler/trunk/debian/bin/runCA 2014-04-23 13:03:24 UTC (rev 16756)
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+BINDIR=/usr/lib/wgs-assembler
+
+# make sure tools like tg_index.bin will be found
+export PATH=$BINDIR:$PATH
+
+$BINDIR/`basename $0` $@
Modified: trunk/packages/wgs-assembler/trunk/debian/control
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/control 2014-04-23 12:51:43 UTC (rev 16755)
+++ trunk/packages/wgs-assembler/trunk/debian/control 2014-04-23 13:03:24 UTC (rev 16756)
@@ -17,7 +17,8 @@
Package: wgs-assembler
Architecture: any
Depends: ${shlibs:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ tcsh
Description: Whole-Genome DNA sequence assembler
Celera Assembler is scientific software for DNA research. It can
reconstruct long sequences of genomic DNA given the fragmentary data
@@ -58,3 +59,16 @@
It provides tools for searching (ESTs, mRNAs, sequencing reads);
aligning (ESTs, mRNAs, whole genomes); and a variety of analyses
based on kmers.
+
+Package: libwgs-kmer-dev
+Architecture: any
+Section: libdevel
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+Description: suite of tools for DNA sequence analysis (development lib)
+ The kmer package is a suite of tools for DNA sequence analysis.
+ It provides tools for searching (ESTs, mRNAs, sequencing reads);
+ aligning (ESTs, mRNAs, whole genomes); and a variety of analyses
+ based on kmers.
+ .
+ This package contains the static libraries and header files.
Added: trunk/packages/wgs-assembler/trunk/debian/libwgs-kmer-dev.install
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/libwgs-kmer-dev.install (rev 0)
+++ trunk/packages/wgs-assembler/trunk/debian/libwgs-kmer-dev.install 2014-04-23 13:03:24 UTC (rev 16756)
@@ -0,0 +1,2 @@
+kmer/installdir/lib usr
+kmer/installdir/include/* usr/include/kmer
Modified: trunk/packages/wgs-assembler/trunk/debian/patches/format-security.patch
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/patches/format-security.patch 2014-04-23 12:51:43 UTC (rev 16755)
+++ trunk/packages/wgs-assembler/trunk/debian/patches/format-security.patch 2014-04-23 13:03:24 UTC (rev 16756)
@@ -1,3 +1,7 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 17 Apr 2014 15:04:22 +0200
+Description: Fix issues when building using -Wformat-security
+
--- a/src/AS_REZ/StatisticsREZ.C
+++ b/src/AS_REZ/StatisticsREZ.C
@@ -639,7 +639,7 @@ void print_all_scaffold_walk_stat_struct
Modified: trunk/packages/wgs-assembler/trunk/debian/rules
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/rules 2014-04-23 12:51:43 UTC (rev 16755)
+++ trunk/packages/wgs-assembler/trunk/debian/rules 2014-04-23 13:03:24 UTC (rev 16756)
@@ -4,39 +4,37 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+
%:
dh $@
override_dh_auto_build:
-# # gmake is hard coded in too many places
-# cd kmer; ln -s /usr/bin/make gmake
-# cd src; ln -s /usr/bin/make gmake
-# # get a few file that would otherwise be missed
-# export PATH=$$PATH:.; cd kmer; sh configure.sh;
-# cd kmer/build ; ln -s ../Make.compilers . ; make makepath
-# cd kmer; ln -sf build/makepath.pl build/makepath build/makepath.c .
-# cd kmer; export PATH=$$PATH:.; make install
-# cd kmer; ln -sf Linux-* installdir
-
# do stuff for kmer
- cd kmer && sh configure.sh && SAMTOOLS=/usr/include/samtools make install && ln -sf Linux-* installdir
+ cd kmer && sh configure.sh && SAMTOOLS=/usr/include/samtools $(MAKE) install && ln -sf Linux-* installdir
# do stuff for wgs-assembler
$(MAKE) -C src
ln -sf Linux-* installdir
override_dh_install:
- find ./* -print
- mkdir -p $(CURDIR)/debian/wgs-kmer/usr/bin
- mkdir -p $(CURDIR)/debian/wgs-kmer/usr/include/kmer
- cp -r installdir/bin/* $(CURDIR)/debian/wgs-assembler/usr/bin/
- cp -r kmer/installdir/bin/* $(CURDIR)/debian/wgs-kmer/usr/bin/
- cp -r kmer/installdir/include/* $(CURDIR)/debian/wgs-kmer/usr/include/kmer/
+ dh_install
+ for pm in `grep -l '#!/usr/local/bin/' debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)/* 2>/dev/null` ; do \
+ sed -i 's?#!/usr/local/bin/?#!/usr/bin/?' $${pm} ; \
+ done
-#
-#clean::
-# rm -rf kmer/makepath.pl kmer/installdir kmer/build/Make.compilers installdir
+override_dh_auto_clean:
+ cd kmer && $(MAKE) clean
+ $(MAKE) -C src clean
+ rm -rf Linux-* installdir
+ rm -rf kmer/Linux-* kmer/installdir kmer/Make.compilers
+ find kmer -name "*.d" -delete
+override_dh_fixperms:
+ dh_fixperms
+ chmod -x debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)/TIGR/*
+ chmod -x debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)/caqc_help.ini
+
get-orig-source:
mkdir -p ../tarballs
- uscan --verbose --force-download --repack --repack-compression bz2 --destdir=../tarballs
+ uscan --verbose --force-download --repack --compression bz2 --destdir=../tarballs
Deleted: trunk/packages/wgs-assembler/trunk/debian/wgs-assembler.dirs
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/wgs-assembler.dirs 2014-04-23 12:51:43 UTC (rev 16755)
+++ trunk/packages/wgs-assembler/trunk/debian/wgs-assembler.dirs 2014-04-23 13:03:24 UTC (rev 16756)
@@ -1,2 +0,0 @@
-usr/include/kmer
-usr/bin
Added: trunk/packages/wgs-assembler/trunk/debian/wgs-assembler.install
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/wgs-assembler.install (rev 0)
+++ trunk/packages/wgs-assembler/trunk/debian/wgs-assembler.install 2014-04-23 13:03:24 UTC (rev 16756)
@@ -0,0 +1,2 @@
+installdir/bin/* usr/lib/wgs-assembler
+debian/bin usr
Added: trunk/packages/wgs-assembler/trunk/debian/wgs-kmer.install
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/wgs-kmer.install (rev 0)
+++ trunk/packages/wgs-assembler/trunk/debian/wgs-kmer.install 2014-04-23 13:03:24 UTC (rev 16756)
@@ -0,0 +1 @@
+kmer/installdir/bin usr
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