[med-svn] r9992 - in trunk/packages/wgs-assembler/trunk/debian: . patches
Thorsten Alteholz
alteholz at alioth.debian.org
Tue Mar 13 18:44:24 UTC 2012
Author: alteholz
Date: 2012-03-13 18:44:24 +0000 (Tue, 13 Mar 2012)
New Revision: 9992
Added:
trunk/packages/wgs-assembler/trunk/debian/patches/
trunk/packages/wgs-assembler/trunk/debian/patches/make-implicit.patch
trunk/packages/wgs-assembler/trunk/debian/patches/series
Modified:
trunk/packages/wgs-assembler/trunk/debian/changelog
trunk/packages/wgs-assembler/trunk/debian/control
trunk/packages/wgs-assembler/trunk/debian/copyright
trunk/packages/wgs-assembler/trunk/debian/rules
Log:
some progress here, but not yet finished
Modified: trunk/packages/wgs-assembler/trunk/debian/changelog
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/changelog 2012-03-13 18:40:55 UTC (rev 9991)
+++ trunk/packages/wgs-assembler/trunk/debian/changelog 2012-03-13 18:44:24 UTC (rev 9992)
@@ -9,9 +9,9 @@
* debian/watch: new tarballs are compressed with bz2
* debian/rules: target get-orig-source added
* debian/control: debhelper changed to 8.0
- * debian/control: standards version changed to 3.9.2 (no other changes)
+ * debian/control: standards version changed to 3.9.3 (no other changes)
* debian/control: VCS fields updated
* Initial release (Closes: #395843)
- -- William Spooner <whs at eaglegenomics.com> Sat, 29 Jan 2011 16:40:00 +0000
+ -- Thorsten Alteholz <debian at alteholz.de> Mon, 05 Mar 2012 18:40:00 +0100
Modified: trunk/packages/wgs-assembler/trunk/debian/control
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/control 2012-03-13 18:40:55 UTC (rev 9991)
+++ trunk/packages/wgs-assembler/trunk/debian/control 2012-03-13 18:44:24 UTC (rev 9992)
@@ -1,11 +1,12 @@
Source: wgs-assembler
Section: science
Priority: extra
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: William Spooner <whs at eaglegenomics.com>,
- Andreas Tille <tille at debian.org>
+ Andreas Tille <tille at debian.org>,
+ Thorsten Alteholz <debian at alteholz.de>
Build-Depends: debhelper (>= 8.0.0), libbz2-dev
-Standards-Version: 3.9.2
+Standards-Version: 3.9.3
Homepage: http://wgs-assembler.sourceforge.net
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/wgs-assembler/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/wgs-assembler/trunk/
@@ -19,5 +20,16 @@
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.
+ historic value. It was licensed as open source and since extended
+ to provide hybrid assemblies across an expanding number of sequence
+ types.
+
+Package: wgs-kmer
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, wgs-assembler
+Provides: kmer
+Description: suite of tools for DNA sequence analysis
+ 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.
Modified: trunk/packages/wgs-assembler/trunk/debian/copyright
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/copyright 2012-03-13 18:40:55 UTC (rev 9991)
+++ trunk/packages/wgs-assembler/trunk/debian/copyright 2012-03-13 18:44:24 UTC (rev 9992)
@@ -1,4 +1,4 @@
-Format: http://dep.debian.net/deps/dep5/
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0
Upstream-Name: WGS-Assembler
Upstream-Contact: Brian Walenz
Source: http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/
@@ -13,23 +13,28 @@
R. L. Strausberg, C. A. Saski, D. Lawson,
F. H. Collins, F. C. Kafatos, G. K. Christophides,
S. W. Clifton, E. F. Kirkness and N. J. Besansky
-
License: GPL-2+
+ wgs-assembler is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ Velvet is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with Velvet; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
- wgs-assembler is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- Velvet is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with Velvet; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
Files: debian/*
-Copyright: © 2011 William Spooner <whs at eaglegenomics.com>,
+Copyright: © 2011-2012 William Spooner <whs at eaglegenomics.com>,
Andreas Tille <tille at debian.org>,
+ Thorsten Alteholz <debian at alteholz.de>
+License: GPL-2+
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
Added: trunk/packages/wgs-assembler/trunk/debian/patches/make-implicit.patch
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/patches/make-implicit.patch (rev 0)
+++ trunk/packages/wgs-assembler/trunk/debian/patches/make-implicit.patch 2012-03-13 18:44:24 UTC (rev 9992)
@@ -0,0 +1,27 @@
+Description: do not use compile flag -Wimplicit with g++
+Author: Thorsten Alteholz <debian at alteholz.de>
+Index: wgs-7.0/src/c_make.as
+===================================================================
+--- wgs-7.0.orig/src/c_make.as 2011-12-29 10:10:30.000000000 +0100
++++ wgs-7.0/src/c_make.as 2012-03-09 14:18:17.000000000 +0100
+@@ -65,17 +65,17 @@
+ ifeq ($(OSTYPE), Linux)
+ ifeq ($(MACHINETYPE), i686)
+ ARCH_LDFLAGS += -pthread -lm
+- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
++ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
+ ARCH_LIB = /usr/X11R6/lib
+ endif
+ ifeq ($(MACHINETYPE), amd64)
+ ARCH_LDFLAGS += -pthread -lm
+- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
++ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
+ ARCH_LIB = /usr/lib64 /usr/X11R6/lib64
+ endif
+ ifeq ($(MACHINETYPE), ia64)
+ ARCH_LDFLAGS += -pthread -lm
+- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
++ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
+ ARCH_LIB = /usr/X11R6/lib
+ endif
+
Added: trunk/packages/wgs-assembler/trunk/debian/patches/series
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/patches/series (rev 0)
+++ trunk/packages/wgs-assembler/trunk/debian/patches/series 2012-03-13 18:44:24 UTC (rev 9992)
@@ -0,0 +1 @@
+make-implicit.patch
Modified: trunk/packages/wgs-assembler/trunk/debian/rules
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/rules 2012-03-13 18:40:55 UTC (rev 9991)
+++ trunk/packages/wgs-assembler/trunk/debian/rules 2012-03-13 18:44:24 UTC (rev 9992)
@@ -1,10 +1,5 @@
#!/usr/bin/make -f
# -*- makefile -*-
-# Sample debian/rules that uses debhelper.
-# This file was originally written by Joey Hess and Craig Small.
-# As a special exception, when this file is copied by dh-make into a
-# dh-make output file, you may use that output file without restriction.
-# This special exception was added by Craig Small in version 0.37 of dh-make.
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
@@ -13,25 +8,35 @@
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
+# # 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
+ cd kmer; make install
cd kmer; 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-assembler/usr/bin/
- cp -r kmer/installdir/include/* $(CURDIR)/debian/wgs-assembler/usr/include/kmer/
+ cp -r kmer/installdir/bin/* $(CURDIR)/debian/wgs-kmer/usr/bin/
+ cp -r kmer/installdir/include/* $(CURDIR)/debian/wgs-kmer/usr/include/kmer/
-clean::
- rm -rf kmer/makepath.pl kmer/installdir kmer/build/Make.compilers installdir
+#
+#clean::
+# rm -rf kmer/makepath.pl kmer/installdir kmer/build/Make.compilers installdir
get-orig-source:
mkdir -p ../tarballs
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