[med-svn] r13049 - in trunk/packages: . mach mach/trunk mach/trunk/debian mach/trunk/debian/patches mach/trunk/debian/source
Steffen Möller
moeller at alioth.debian.org
Tue Feb 19 15:48:51 UTC 2013
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 <moeller at debian.org> 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 <moeller at debian.org> 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 <moeller at debian.org>
+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 <moeller at debian.org>
+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
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