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 <[email protected]> Sat, 29 Jan 2011 16:40:00 +0000 + -- Thorsten Alteholz <[email protected]> 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 <[email protected]> +Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: William Spooner <[email protected]>, - Andreas Tille <[email protected]> + Andreas Tille <[email protected]>, + Thorsten Alteholz <[email protected]> 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 <[email protected]>, +Copyright: © 2011-2012 William Spooner <[email protected]>, Andreas Tille <[email protected]>, + Thorsten Alteholz <[email protected]> +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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
