Author: moeller Date: 2013-02-19 15:48:51 +0000 (Tue, 19 Feb 2013) New Revision: 13049
Added: trunk/packages/mach/ trunk/packages/mach/trunk/ trunk/packages/mach/trunk/debian/ trunk/packages/mach/trunk/debian/README.Debian trunk/packages/mach/trunk/debian/changelog trunk/packages/mach/trunk/debian/compat trunk/packages/mach/trunk/debian/control trunk/packages/mach/trunk/debian/copyright trunk/packages/mach/trunk/debian/docs trunk/packages/mach/trunk/debian/mach-haplotyper.dirs trunk/packages/mach/trunk/debian/mach-haplotyper.links trunk/packages/mach/trunk/debian/mach1.1 trunk/packages/mach/trunk/debian/manpages trunk/packages/mach/trunk/debian/patches/ trunk/packages/mach/trunk/debian/patches/Makefile.patch trunk/packages/mach/trunk/debian/patches/series trunk/packages/mach/trunk/debian/rules trunk/packages/mach/trunk/debian/source/ trunk/packages/mach/trunk/debian/source/format trunk/packages/mach/trunk/debian/watch Log: It is one of those tools that cannot be redistributed, but it can be packaged for local purposes. Other than VMD or ROSETTA, mach comes with a working watch file. We could as such auto-create the package, if some good soul only prepares a proper download script that also performes the repackaging because of the multiple topdirs. Added: trunk/packages/mach/trunk/debian/README.Debian =================================================================== --- trunk/packages/mach/trunk/debian/README.Debian (rev 0) +++ trunk/packages/mach/trunk/debian/README.Debian 2013-02-19 15:48:51 UTC (rev 13049) @@ -0,0 +1,6 @@ +mach-haplotyper for Debian +-------------------------- + +This package cannot be redistributed. + + -- Steffen Moeller <[email protected]> Tue, 19 Feb 2013 14:16:48 +0100 Added: trunk/packages/mach/trunk/debian/changelog =================================================================== --- trunk/packages/mach/trunk/debian/changelog (rev 0) +++ trunk/packages/mach/trunk/debian/changelog 2013-02-19 15:48:51 UTC (rev 13049) @@ -0,0 +1,6 @@ +mach-haplotyper (1.0.18-1) UNRELEASED; urgency=low + + * This package is not released. Packaging instructions are only for + internal use. + + -- Steffen Moeller <[email protected]> Tue, 19 Feb 2013 14:16:48 +0100 Added: trunk/packages/mach/trunk/debian/compat =================================================================== --- trunk/packages/mach/trunk/debian/compat (rev 0) +++ trunk/packages/mach/trunk/debian/compat 2013-02-19 15:48:51 UTC (rev 13049) @@ -0,0 +1 @@ +8 Added: trunk/packages/mach/trunk/debian/control =================================================================== --- trunk/packages/mach/trunk/debian/control (rev 0) +++ trunk/packages/mach/trunk/debian/control 2013-02-19 15:48:51 UTC (rev 13049) @@ -0,0 +1,17 @@ +Source: mach-haplotyper +Section: non-free/science +Priority: extra +Maintainer: Steffen Moeller <[email protected]> +Build-Depends: debhelper (>= 8.0.0), dpkg-dev (>= 1.16.1~) +Standards-Version: 3.9.4 +Homepage: http://www.sph.umich.edu/csg/abecasis/MACH/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mach-haplotyper/trunk/ +Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/mach-haplotyper/trunk/ + +Package: mach-haplotyper +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: Markov Chain based SNP haplotyper + Recent advancements in chip-based DNA genotyping allow to infer DNA + variants that are not part of the chip but known to be associated + with a combination of SNPs that are measured. Added: trunk/packages/mach/trunk/debian/copyright =================================================================== --- trunk/packages/mach/trunk/debian/copyright (rev 0) +++ trunk/packages/mach/trunk/debian/copyright 2013-02-19 15:48:51 UTC (rev 13049) @@ -0,0 +1,28 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: mach-haplotyper +Source: http://www.sph.umich.edu/csg/abecasis/MACH/download/ + +Files: * +Copyright: <years> <put author's name and email here> + <years> <likewise for another author> +License: + not redistributable + +Files: debian/* +Copyright: 2013 Steffen Moeller <[email protected]> +License: GPL-2+ + This package 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. + . + This package 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 this program. If not, see <http://www.gnu.org/licenses/> + . + 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/mach/trunk/debian/docs =================================================================== Added: trunk/packages/mach/trunk/debian/mach-haplotyper.dirs =================================================================== --- trunk/packages/mach/trunk/debian/mach-haplotyper.dirs (rev 0) +++ trunk/packages/mach/trunk/debian/mach-haplotyper.dirs 2013-02-19 15:48:51 UTC (rev 13049) @@ -0,0 +1 @@ +usr/bin Added: trunk/packages/mach/trunk/debian/mach-haplotyper.links =================================================================== --- trunk/packages/mach/trunk/debian/mach-haplotyper.links (rev 0) +++ trunk/packages/mach/trunk/debian/mach-haplotyper.links 2013-02-19 15:48:51 UTC (rev 13049) @@ -0,0 +1 @@ +usr/share/man/man1/mach1.1 usr/share/man/man1/thunder.1 Added: trunk/packages/mach/trunk/debian/mach1.1 =================================================================== --- trunk/packages/mach/trunk/debian/mach1.1 (rev 0) +++ trunk/packages/mach/trunk/debian/mach1.1 2013-02-19 15:48:51 UTC (rev 13049) @@ -0,0 +1,12 @@ +.\" Hey, EMACS: -*- nroff -*- +.TH MACH-HAPLOTYPER 1 "February 19, 2013" +.SH NAME +mach \- haplotyping and imputation of SNPs +.SH SYNOPSIS +.B mach1 +.br +.B thunder +.SH DESCRIPTION +Some good soul please provide a man page for MACH. +.SH SEE ALSO +.BR http://www.sph.umich.edu/csg/abecasis/MACH Added: trunk/packages/mach/trunk/debian/manpages =================================================================== --- trunk/packages/mach/trunk/debian/manpages (rev 0) +++ trunk/packages/mach/trunk/debian/manpages 2013-02-19 15:48:51 UTC (rev 13049) @@ -0,0 +1 @@ +debian/mach1.1 Added: trunk/packages/mach/trunk/debian/patches/Makefile.patch =================================================================== --- trunk/packages/mach/trunk/debian/patches/Makefile.patch (rev 0) +++ trunk/packages/mach/trunk/debian/patches/Makefile.patch 2013-02-19 15:48:51 UTC (rev 13049) @@ -0,0 +1,43 @@ +Index: mach-haplotyper-1.0.18/Makefile +=================================================================== +--- mach-haplotyper-1.0.18.orig/Makefile ++++ mach-haplotyper-1.0.18/Makefile +@@ -16,7 +16,7 @@ + # + # CFLAGS=-O2 -I./libsrc/ -I./mach1 + # +-CFLAGS=-O2 -static -I./libsrc -I./mach1 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE ++CFLAGS +=-O2 -I./libsrc -I./mach1 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE + + # executable file names and locations + BINDIR = executables +@@ -89,10 +89,10 @@ + + # dependencies for executables + $(MACH) : $(LIBFILE) $(MACHOBJ) $(BINDIR) +- $(CXX) $(CFLAGS) -o $@ $(MACHOBJ) $(LIBFILE) -lm -lz ++ $(CXX) $(LDFLAGS) $(CFLAGS) -o $@ $(MACHOBJ) $(LIBFILE) -lm -lz + + $(THUNDER) : $(LIBFILE) $(THUNDEROBJ) $(BINDIR) +- $(CXX) $(CFLAGS) -o $@ $(THUNDEROBJ) $(LIBFILE) -lm -lz ++ $(CXX) $(LDFLAGS) $(CFLAGS) -o $@ $(THUNDEROBJ) $(LIBFILE) -lm -lz + + $(BINDIR) : + mkdir $(BINDIR) +@@ -142,13 +142,13 @@ + cd $(DISTRIBDIR); csh ../stamp MaCH + + .c.o : +- $(CXX) $(CFLAGS) -o $@ -c $*.c ++ $(CXX) $(CPPFLAGS) $(CFLAGS) -o $@ -c $*.c + + .cpp.X.o : +- $(CXX) $(CFLAGS) -o $@ -c $*.cpp -DVERSION=\"$(VERSION)\" -D__CHROMOSOME_X__ ++ $(CXX) $(CPPFLAGS) $(CFLAGS) -o $@ -c $*.cpp -DVERSION=\"$(VERSION)\" -D__CHROMOSOME_X__ + + .cpp.o : +- $(CXX) $(CFLAGS) -o $@ -c $*.cpp -DVERSION=\"$(VERSION)\" ++ $(CXX) $(CPPFLAGS) $(CFLAGS) -o $@ -c $*.cpp -DVERSION=\"$(VERSION)\" + + archive : clean + mkdir -p mach-$(VERSION) Added: trunk/packages/mach/trunk/debian/patches/series =================================================================== --- trunk/packages/mach/trunk/debian/patches/series (rev 0) +++ trunk/packages/mach/trunk/debian/patches/series 2013-02-19 15:48:51 UTC (rev 13049) @@ -0,0 +1 @@ +Makefile.patch Added: trunk/packages/mach/trunk/debian/rules =================================================================== --- trunk/packages/mach/trunk/debian/rules (rev 0) +++ trunk/packages/mach/trunk/debian/rules 2013-02-19 15:48:51 UTC (rev 13049) @@ -0,0 +1,17 @@ +#!/usr/bin/make -f +# -*- makefile -*- + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +DPKG_EXPORT_BUILDFLAGS = 1 +include /usr/share/dpkg/buildflags.mk + +%: + dh $@ + +override_dh_auto_build: + $(MAKE) all + +override_dh_auto_install: + $(MAKE) install INSTALLDIR=$(CURDIR)/debian/mach-haplotyper/usr/bin/ Property changes on: trunk/packages/mach/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/mach/trunk/debian/source/format =================================================================== --- trunk/packages/mach/trunk/debian/source/format (rev 0) +++ trunk/packages/mach/trunk/debian/source/format 2013-02-19 15:48:51 UTC (rev 13049) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/mach/trunk/debian/watch =================================================================== --- trunk/packages/mach/trunk/debian/watch (rev 0) +++ trunk/packages/mach/trunk/debian/watch 2013-02-19 15:48:51 UTC (rev 13049) @@ -0,0 +1,2 @@ +version=3 +http://www.sph.umich.edu/csg/abecasis/MACH/download/mach\.([0-9.]*)\.source.tgz _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
