[med-svn] r1814 - in trunk/packages/muscle/branches: . libmuscle libmuscle/debian
tille at alioth.debian.org
tille at alioth.debian.org
Tue Apr 29 16:10:34 UTC 2008
Author: tille
Date: 2008-04-29 16:10:30 +0000 (Tue, 29 Apr 2008)
New Revision: 1814
Added:
trunk/packages/muscle/branches/libmuscle/
trunk/packages/muscle/branches/libmuscle/debian/
trunk/packages/muscle/branches/libmuscle/debian/README.Debian
trunk/packages/muscle/branches/libmuscle/debian/changelog
trunk/packages/muscle/branches/libmuscle/debian/compat
trunk/packages/muscle/branches/libmuscle/debian/control
trunk/packages/muscle/branches/libmuscle/debian/copyright
trunk/packages/muscle/branches/libmuscle/debian/d-devlibdeps
trunk/packages/muscle/branches/libmuscle/debian/d-shlibmove
trunk/packages/muscle/branches/libmuscle/debian/get-orig-source
trunk/packages/muscle/branches/libmuscle/debian/muscle.1
trunk/packages/muscle/branches/libmuscle/debian/muscle.1.xml
trunk/packages/muscle/branches/libmuscle/debian/muscle.install
trunk/packages/muscle/branches/libmuscle/debian/muscle.manpages
trunk/packages/muscle/branches/libmuscle/debian/rules
trunk/packages/muscle/branches/libmuscle/debian/watch
Log:
Potential candidate for a replacement of current muscle package. PLEASE TEST!
Added: trunk/packages/muscle/branches/libmuscle/debian/README.Debian
===================================================================
--- trunk/packages/muscle/branches/libmuscle/debian/README.Debian (rev 0)
+++ trunk/packages/muscle/branches/libmuscle/debian/README.Debian 2008-04-29 16:10:30 UTC (rev 1814)
@@ -0,0 +1,13 @@
+libMUSCLE for Debian
+--------------------
+
+This library is packaged as a precondition of the Mauve
+multiple genome alignment package.
+
+Please note that the Author of this package Aaron Darling <darling at cs.wisc.edu>
+has obtained the original source file for MUSCLE 3.7 from
+ http://www.drive5.com/muscle/download3.6.html
+and has changed the build system to turn MUSCLE into a library which can
+be used for libMems.
+
+ -- Andreas Tille <tille at debian.org> Thu, 14 Feb 2008 22:13:45 +0100
Added: trunk/packages/muscle/branches/libmuscle/debian/changelog
===================================================================
--- trunk/packages/muscle/branches/libmuscle/debian/changelog (rev 0)
+++ trunk/packages/muscle/branches/libmuscle/debian/changelog 2008-04-29 16:10:30 UTC (rev 1814)
@@ -0,0 +1,88 @@
+libmuscle (1:3.7.20080422-1) UNRELEASED; urgency=low
+
+ * New packaging with separate dynamical library based on the work
+ of Aaron Darling
+
+ -- Andreas Tille <tille at debian.org> Tue, 22 Apr 2008 14:35:32 +0200
+
+muscle (3.70+fix1-2) unstable; urgency=low
+
+ * debian/control Conflicts: and Replaces: muscle-doc (Closes: #465607)
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Thu, 14 Feb 2008 10:44:17 +0900
+
+muscle (3.70+fix1-1) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * New upstream version, buildable with GCC 4.3 (Closes: #462707)
+ The version number was not increased upstream when the sources were
+ changed. We name this new version in Debian "3.70+fix1".
+ * Updated manual page.
+ * Converted the source package to CDBS, dropped Makefile patch.
+ * Fused muscle and muscle-doc.
+
+ [ Nelson A. de Oliveira ]
+ * Fixed watch file (Closes: #462827)
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 06 Feb 2008 12:04:31 +0900
+
+muscle (3.70-1) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * New upstream release (bugfixes plus undocumented new features).
+ * debian/control:
+ - Add Subversion repository.
+ - Swiched to quilt.
+ - Enhaces: seaview because SeaView can call muscle to re-align sequences.
+ - Moved the Homepage: field out from the package's description.
+ - Using debhelper 5.
+ - Removed [Biology] from package description as there are Debtags now.
+ - Checked that muscle conforms to Policy 3.7.3.
+ - Updated Steffen's email address.
+ * Handling nostrip build option (policy 10.1) (Closes: #437599).
+ * Updated manpage.
+ * debian/copyright made machine-readable.
+
+ [ Nelson A. de Oliveira ]
+ * Added watch file.
+
+ [ David Paleino ]
+ * debian/manpage.xml moved to debian/muscle.1.xml
+ * debian/muscle.1 added - statically built
+ * debian/manpages removed - passing arguments to dh_installman
+ directly
+ * debian/control:
+ - B-D updated (see above)
+ - added myself to Uploaders
+ - moved XS-Vcs-* to Vcs-*
+ * debian/rules:
+ - manpages statically built
+ - minor changes
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 12 Jan 2008 16:55:48 +0900
+
+muscle (3.60-1) unstable; urgency=low
+
+ * New upstram release (Closes: Bug#361742).
+ * New maintainers email addresses.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 5 Aug 2006 09:57:27 +0900
+
+muscle (3.52-2) unstable; urgency=low
+
+ * Added missing build dependencies (Closes: Bug#287684).
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Wed, 29 Dec 2004 21:50:47 +0200
+
+muscle (3.52-1) unstable; urgency=low
+
+ * New upstream version.
+ * Fix build on arch other than Pentium (Closes: Bug#285000).
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Sun, 18 Dec 2004 00:06:00 +0200
+
+muscle (3.51-1) unstable; urgency=low
+
+ * Initial Release (Closes: Bug#280411).
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Sun, 19 Sep 2004 00:51:19 +0200
Added: trunk/packages/muscle/branches/libmuscle/debian/compat
===================================================================
--- trunk/packages/muscle/branches/libmuscle/debian/compat (rev 0)
+++ trunk/packages/muscle/branches/libmuscle/debian/compat 2008-04-29 16:10:30 UTC (rev 1814)
@@ -0,0 +1 @@
+6
Added: trunk/packages/muscle/branches/libmuscle/debian/control
===================================================================
--- trunk/packages/muscle/branches/libmuscle/debian/control (rev 0)
+++ trunk/packages/muscle/branches/libmuscle/debian/control 2008-04-29 16:10:30 UTC (rev 1814)
@@ -0,0 +1,51 @@
+Source: libmuscle
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 6), autotools-dev, d-shlibs (>= 0.38), cdbs, quilt, doxygen
+Standards-Version: 3.7.3
+Section: libs
+Homepage: http://asap.ahabs.wisc.edu/software/software-development-libraries/libmuscle.html
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/muscle/branches/libmuscle/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/muscle/branches/libmuscle
+
+Package: libmuscle-3.7-1-dev
+Section: libdevel
+Architecture: any
+Depends: libmuscle-3.7-1 (= ${binary:Version}), ${devlibs:Depends}
+Provides: libmuscle-3.7-dev
+Conflicts: libmuscle-3.7-dev
+Description: multiple alignment of protein sequences library
+ libMUSCLE is library that is used by MUSCLE a multiple alignment program
+ for protein sequences. MUSCLE stands for multiple sequence comparison by
+ log-expectation. In the authors tests, MUSCLE achieved the highest scores
+ of all tested programs on several alignment accuracy benchmarks, and is
+ also one of the fastest programs out there.
+
+Package: libmuscle-3.7-1
+Section: libs
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: multiple alignment of protein sequences library
+ libMUSCLE is library that is used by MUSCLE a multiple alignment program
+ for protein sequences. MUSCLE stands for multiple sequence comparison by
+ log-expectation. In the authors tests, MUSCLE achieved the highest scores
+ of all tested programs on several alignment accuracy benchmarks, and is
+ also one of the fastest programs out there.
+ .
+ This package contains the dynamic library.
+
+Package: muscle
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Conflicts: muscle-doc
+Replaces: muscle-doc
+Provides: muscle-doc
+Enhances: seaview
+Description: Multiple alignment program of protein sequences
+ MUSCLE is a multiple alignment program for protein sequences. MUSCLE
+ stands for multiple sequence comparison by log-expectation. In the
+ authors tests, MUSCLE achieved the highest scores of all tested
+ programs on several alignment accuracy benchmarks, and is also one of
+ the fastest programs out there.
Added: trunk/packages/muscle/branches/libmuscle/debian/copyright
===================================================================
--- trunk/packages/muscle/branches/libmuscle/debian/copyright (rev 0)
+++ trunk/packages/muscle/branches/libmuscle/debian/copyright 2008-04-29 16:10:30 UTC (rev 1814)
@@ -0,0 +1,31 @@
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Andreas Tille <tille at debian.org>
+X-Debianized-Date: Thu, 28 Feb 2008 20:13:45 +0100
+X-Source-Downloaded-From: http://gel.ahabs.wisc.edu/mauve/source/snapshots
+X-Upstream-Author: Aaron Darling <darling at cs.wisc.edu>
+
+Source: http://asap.ahabs.wisc.edu/software/software-development-libraries/libmuscle.html
+
+Files: debian/*
+Copyright: © 2008, Andreas Tille <tille 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.
+ .
+ On Debian systems, the complete text of the licenses can be found in:
+ GPL-2 - `/usr/share/common-licenses/GPL-2'
+
+Files: libMUSCLE/*
+Copyright: This work in not subjected to copyright.
+X-Comment: This is the work (2004-2007 )of Robert C. Edgar "Bob" <muscle at drive5.com>
+ It is provided separately as Public Domain from
+ http://www.drive5.com/muscle/download3.6.html
+ and was turned into a library by Aaron Darling <darling at cs.wisc.edu>
+ (see below)
+
+Files: *, projects, m4
+Copyright: This work in not subjected to copyright.
+X-Comment: The MUSCLE project was turned into a library by
+ Aaron Darling <darling at cs.wisc.edu>
Added: trunk/packages/muscle/branches/libmuscle/debian/d-devlibdeps
===================================================================
--- trunk/packages/muscle/branches/libmuscle/debian/d-devlibdeps (rev 0)
+++ trunk/packages/muscle/branches/libmuscle/debian/d-devlibdeps 2008-04-29 16:10:30 UTC (rev 1814)
@@ -0,0 +1,199 @@
+#!/bin/bash
+# d-devlibdeps -- get list of build-time dependencies
+# Copyright (C) 2002-2005 Junichi Uekawa
+#
+# This program 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 program 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, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+# 2002 May 3. Created.
+# automatic depends line generator.
+
+set -e
+set -o pipefail
+
+function getname () {
+ local SONAMELIBNAME
+ local SONAMEVERSION
+ local SONAME
+ SONAME="$1"
+ SONAMELIBNAME=$(echo $SONAME | sed 's/\.so\..*$//')
+ SONAMEVERSION=$(echo $SONAME | sed 's/^.*\.so\.//')
+ case "$SONAMELIBNAME" in
+ *[0-9])
+ RETURN="$SONAMELIBNAME-$SONAMEVERSION"
+ ;;
+ *)
+ RETURN="$SONAMELIBNAME$SONAMEVERSION"
+ ;;
+ esac
+}
+
+function overridedevlibdeps () {
+ # overrides necessary until the scheme is adopted.
+ sed \
+ -e 's/libX11-6-dev/libx11-dev | xlibs-dev (<< 4.3.0)/' \
+ -e 's/libXext6-dev/libxext-dev | xlibs-dev (<< 4.3.0)/' \
+ -e 's/libXi6-dev/libxi-dev | xlibs-dev (<< 4.3.0)/' \
+ -e 's/libXpm4-dev/libxpm-dev | xlibs-dev (<< 4.3.0)/' \
+ -e 's/libICE6-dev/libice-dev | xlibs-dev (<< 4.3.0)/' \
+ -e 's/libSM6-dev/libsm-dev | xlibs-dev (<< 4.3.0)/' \
+ -e 's/libGL1-dev/xlibmesa-gl-dev | xlibs-dev (<< 4.3.0)/' \
+ -e 's/libGLU1-dev/xlibmesa-glu-dev | xlibs-dev (<< 4.3.0)/' \
+ -e 's/libcrypt1-dev//' \
+ -e 's/libcrypt1\.1-dev//' \
+ -e 's/libdl2-dev//' \
+ -e 's/libdl2.1-dev//' \
+ -e 's/libm6-dev//' \
+ -e 's/libm6.1-dev//' \
+ -e 's/libm1-dev//' \
+ -e 's/libnsl1-dev//' \
+ -e 's/libnsl1\.1-dev//' \
+ -e 's/libpthread0-dev//' \
+ -e 's/libpthread0\.3-dev//' \
+ -e 's/libpthread.*-dev/libpthread-dev/' \
+ -e 's/libresolv2-dev//' \
+ -e 's/libglib-1.2-0-dev/libglib1.2-dev/' \
+ -e 's/libgthread-1.2-0-dev/libglib1.2-dev/' \
+ -e 's/libgmodule-1.2-0-dev/libglib1.2-dev/' \
+ -e 's/libgtk-1.2-0-dev/libgtk1.2-dev/' \
+ -e 's/libpam0-dev/libpam0g-dev/' \
+ -e 's/libgdk-1.2-0-dev/libgtk1.2-dev/' \
+ -e 's/libz1-dev/zlib1g-dev/' \
+ -e 's/libgcc_s.*-dev//' \
+ -e 's/libcrypto.*-dev/libssl-dev/' \
+ -e 's/libssl.*-dev/libssl-dev/' \
+ -e 's/libcomerr2//' \
+ -e 's/libcom_err2-dev/comerr-dev/' \
+ -e 's/libgssapi_krb5-2-dev/libkrb5-dev/' \
+ -e 's/libk5crypto3-dev/libkrb5-dev/' \
+ -e 's/libkrb5-3-dev/libkrb5-dev/' \
+ -e 's/libparted-1.6-0-dev/libparted1.6-dev/' \
+ -e 's/libSDL-1.2-0-dev/libsdl1.2-dev/' \
+ -e 's/libvorbis0-dev/libvorbis-dev/' \
+ -e 's/libcrack2-dev/cracklib2-dev/' \
+ -e 's/libkrb1-dev/kerberos4kth-dev/' \
+ -e 's/libtheora0-dev/libtheora-dev/' \
+ -e 's/libvorbisenc2-dev/libvorbis-dev/' \
+ -e 's/libogg0-dev/libogg-dev/' \
+ -e 's/librt1-dev//' \
+ -e 's/libspeex1-dev/libspeex-dev/' \
+ -e 's/libX\(.*\)[0-9]-dev/libx\1-dev/' \
+ -e 's/libgdk-x11-2.0-0-dev/libgtk2.0-dev/' \
+ -e 's/libgdk-x11-2.0-0-dev/libgtk2.0-dev/' \
+ -e 's/libgtk-x11-2.0-0-dev/libgtk2.0-dev/' \
+ -e 's/libgdk_pixbuf-2.0-0-dev/libgtk2.0-dev/' \
+ -e 's/libgd2-dev/libgd-dev/' \
+ -e 's/libgmodule-2.0-0-dev/libglib2.0-dev/' \
+ -e 's/libgobject-2.0-0-dev/libglib2.0-dev/' \
+ -e 's/libglib-2.0-0-dev/libglib2.0-dev/' \
+ -e 's/libpango-1.0-0-dev/libpango1.0-dev/' \
+ -e 's/libpangocairo-1.0-0-dev/libpango1.0-dev/' \
+ -e 's/libatk-1.0-0-dev/libatk1.0-dev/' \
+ -e 's/libxml2-2-dev/libxml2-dev/' \
+ -e 's/libgthread-2.0-0-dev/libglib2.0-dev/' \
+ -e 's/libstdc++6-dev/libstdc++6-4.2-dev/' \
+ "${OVERRIDE[@]/#/-e}" \
+
+
+}
+
+
+function validate_package () {
+# validate if package foo exists, this relies on apt.
+ if [ -z "$1" ]; then
+ # ignore empty.
+ return;
+ fi
+ if grep "^Package: $1\$" debian/control > /dev/null 2> /dev/null ; then
+ # ignore package that is going to be created.
+ echo " --> $1 package from same source package." >&2
+ return
+ fi
+ case $(echo $(apt-cache show $1 2> /dev/null| wc -l ) ) in
+ 0)
+ case $(echo $(apt-cache showpkg $1 2> /dev/null | awk ' /^Reverse Provides: $/,/^$/ {if ($0 !~ /:/) {print $0}}' | wc -l) ) in
+ 0)
+ echo "devlibs error: There is no package matching [$1] and noone provides it, please report bug to d-shlibs maintainer" >&2
+ return 1;;
+ *) echo " --> $1 is provided by a package." >&2 ;;
+ esac;;
+ *) echo " --> $1 package exists." >&2 ;;
+ esac
+ return 0;
+}
+
+while true; do
+ case $1 in
+ --override=*)
+ OVERRIDE[${#OVERRIDE[@]}]="${1/--override=/}"
+ shift;
+ ;;
+ --override)
+ OVERRIDE[${#OVERRIDE[@]}]="$2"
+ shift; shift;
+ ;;
+ --*)
+ #error
+ ;;
+ --|*)
+ break;
+ ;;
+ esac
+done
+
+if [ -z "$2" ]; then
+ echo "$0: Please read manpage for help, not enough options given"
+ exit 1
+fi
+
+OUTPUTFILE="$1"
+shift;
+
+DEPENDS=""
+for A in $*; do
+ # let shell do the delimiting of objdump output./
+ DEPENDS="$DEPENDS $(set -o pipefail; objdump -p ${A} |sed -n 's/^.*NEEDED *//p')"
+done
+
+outputtmp=$(tempfile)
+(
+ set -e
+ if [ -f "$OUTPUTFILE" ] ; then
+ if grep -v "^devlibs:Depends=" "$OUTPUTFILE"; then
+ :
+ fi
+ fi
+ printf "devlibs:Depends="
+ for A in $DEPENDS; do #DEPENDS is a space-delimited thing.
+ getname "$A"
+ echo $RETURN-dev | overridedevlibdeps
+ done | \
+ sort | \
+ uniq | \
+ while read B; do
+ # abuse that only first part of multi-entry overrides is considered
+ if validate_package $B ; then
+ printf "%s " $B ;
+ else
+ echo "ERROR_DEVLIB "
+ fi
+ done | sed -e 's/\([a-z0-9)]\) \+\([a-z]\)/\1, \2/g' -e 's/ \+/ /g' -e 's/^ //' -e 's/ $//'
+ printf "\n"
+) > "${outputtmp}"
+
+if grep "ERROR_DEVLIB" "$outputtmp" > /dev/null; then
+ exit 1
+fi
+
+mv "${outputtmp}" $OUTPUTFILE
Property changes on: trunk/packages/muscle/branches/libmuscle/debian/d-devlibdeps
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/muscle/branches/libmuscle/debian/d-shlibmove
===================================================================
--- trunk/packages/muscle/branches/libmuscle/debian/d-shlibmove (rev 0)
+++ trunk/packages/muscle/branches/libmuscle/debian/d-shlibmove 2008-04-29 16:10:30 UTC (rev 1814)
@@ -0,0 +1,228 @@
+#!/bin/bash
+# d-shlibmove -- move shared library files around for Debian packaging
+# Copyright (C) 2002, 2005 Junichi Uekawa
+#
+# This program 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 program 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, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+# 2002 Apr 23. Created.
+# automatic packaging of libtool-created library packages.
+
+# from d-shlibs package
+
+set -e
+set -o pipefail
+
+function getname () {
+ local SONAMELIBNAME
+ local SONAMEVERSION
+ local SONAME
+ SONAME="$1"
+ SONAMELIBNAME=$(echo $SONAME | sed 's/\.so\..*$//')
+ SONAMEVERSION=$(echo $SONAME | sed 's/^.*\.so\.//')
+ case "$SONAMELIBNAME" in
+ *[0-9])
+ RETURN="$SONAMELIBNAME-$SONAMEVERSION"
+ ;;
+ *)
+ RETURN="$SONAMELIBNAME$SONAMEVERSION"
+ ;;
+ esac
+}
+
+function readlibnameinfo () {
+ LIBNAME="$1"
+
+ if [ -z "$1" ] || ! echo "$1" | grep ".so$" > /dev/null ; then
+ echo "$0: [$1] is not a valid shared library file name " >&2
+ exit 1;
+ fi
+
+ if [ ! -h "$1" ]; then
+ echo "$0: expected [$1] to be a symlink, but it is not" >&2
+ exit 1;
+ fi
+
+ SONAME=$(set -o pipefail; objdump -p ${LIBNAME} |sed -n 's/^.*SONAME *//p' )
+ getname "$SONAME"
+ SONAMEPKGNAME=$(echo "$RETURN" | tr '[A-Z]' '[a-z]')
+ PK=$(basename "$1" | sed 's/\.so$//')
+ PK_LOWER=$(echo ${PK} | tr '[A-Z]' '[a-z]')
+ REALSO=$(readlink -f "${LIBNAME}")
+}
+
+function check_line () {
+ # check line
+ local PKGNAME="$1"
+ local ENTRYLINE="$2"
+
+ if ! awk '/^Package:.*'"$PKGNAME"'/,/^$/{print}' "$CONTROL" | \
+ grep "$ENTRYLINE" > /dev/null; then
+ echo "E: line [$ENTRYLINE] not found in $CONTROL section for $PKGNAME"
+ # set this error signifier to true
+ CHECK_ERROR=true
+ fi
+}
+
+
+echo "Library package automatic movement utility"
+
+CONTROL=debian/control
+
+execscript=$(tempfile)
+INSTALLFILE_SHLPKG=$(tempfile)
+INSTALLFILE_DEVPKG=$(tempfile)
+cat > ${execscript} <<EOF
+set -e
+EOF
+
+DEVLIB_TO_CHECK=
+SUFFIX=
+DEVSUFFIX=
+TRANSITIONSUFFIX=
+
+DOIT=no
+while [ -n "$1" ]; do
+ case $1 in
+ --moveshl)
+ echo "$2 $3" >> "${INSTALLFILE_SHLPKG}"
+ shift; shift; shift;
+ ;;
+ --movedev)
+ echo "$2 $3" >> "${INSTALLFILE_DEVPKG}"
+ shift; shift; shift;
+ ;;
+ --movedevdoc)
+ echo "$2 usr/share/doc/\${PKGDEV}" >> "${INSTALLFILE_DEVPKG}"
+ shift; shift;
+ ;;
+ --commit)
+ DOIT=yes
+ shift;
+ ;;
+ --extralib)
+ readlibnameinfo "$2"
+ DEVLIB_TO_CHECK="${DEVLIB_TO_CHECK} $2"
+ echo "$(dirname $2)/${PK}.a usr/lib" >> "${INSTALLFILE_DEVPKG}"
+ echo "$(dirname $2)/${PK}.la usr/lib || true" >> "${INSTALLFILE_DEVPKG}"
+ echo "$(dirname $2)/${PK}.so usr/lib" >> "${INSTALLFILE_DEVPKG}"
+ echo "$(dirname ${REALSO})/${SONAME} usr/lib" >> "${INSTALLFILE_SHLPKG}"
+ echo "${REALSO} usr/lib" >> "${INSTALLFILE_SHLPKG}"
+
+ shift; shift;
+ ;;
+ --shlibs-local)
+ shift;
+ SHLIBSLOCALVER="$1";
+ shift;
+ ;;
+ --suffix)
+ shift;
+ SUFFIX="$1";
+ shift;
+ ;;
+ --devsuffix)
+ shift;
+ DEVSUFFIX="$1";
+ shift;
+ ;;
+ --c102)
+ TRANSITIONSUFFIX="c102"
+ shift;;
+ --ldbl)
+ TRANSITIONSUFFIX="ldbl"
+ shift;;
+ --override)
+ OVERRIDE[${#OVERRIDE[@]}]="$2"
+ shift; shift;;
+ --|*)
+ break;
+ ;;
+ esac
+done
+
+# path/libxxxx.so.yyy.zz.zz
+# ------------------------- REALSO (actual .so filename that is linked to)
+# -------------- SONAME
+# ------- --- SONAMEPKGNAME (lowercased for package name)
+# --------------- $1
+# ---------- PK
+# ---------- PK_LOWER (lowercased for package name)
+
+DEVLIB_TO_CHECK="${DEVLIB_TO_CHECK} $1"
+readlibnameinfo "$1"
+PKGDEV="${SONAMEPKGNAME}${DEVSUFFIX}-dev"
+PKGSHL="${SONAMEPKGNAME}${SUFFIX}${TRANSITIONSUFFIX}"
+
+INSTALLDIR="install -d -m 755 "
+echo "${INSTALLDIR} debian/${PKGDEV}/usr/lib" >> "$execscript"
+echo "${INSTALLDIR} debian/${PKGSHL}/usr/lib" >> "$execscript"
+echo "mv $(dirname $1)/${PK}.a debian/${PKGDEV}/usr/lib" >> "$execscript"
+echo "mv $(dirname $1)/${PK}.la debian/${PKGDEV}/usr/lib || true" >> "$execscript"
+echo "mv $(dirname $1)/${PK}.so debian/${PKGDEV}/usr/lib" >> "$execscript"
+echo "mv $(dirname ${REALSO})/${SONAME} debian/${PKGSHL}/usr/lib" >> "$execscript"
+echo "mv ${REALSO} debian/${PKGSHL}/usr/lib" >> "$execscript"
+
+if [ -n "${SHLIBSLOCALVER}" ]; then
+ echo "echo \"${SONAMELIBNAME} ${SONAMEVERSION} ${PKGSHL} (>= ${SHLIBSLOCALVER})\" >> debian/shlibs.local" >> "$execscript"
+fi
+
+/bin/bash debian/d-devlibdeps "${OVERRIDE[@]/#/--override=}" debian/"${PKGDEV}".substvars "${DEVLIB_TO_CHECK}"
+
+#do some definition for the file.
+echo "PKGDEV=${PKGDEV}" >> "${execscript}"
+echo "PKGSHL=${PKGSHL}" >> "${execscript}"
+
+#do the extra files
+cat "${INSTALLFILE_SHLPKG}" | while read A B; do
+ echo "${INSTALLDIR} debian/${PKGSHL}/${B}" >> "${execscript}"
+ echo "mv ${A} debian/${PKGSHL}/${B}" >> "${execscript}"
+done
+cat "${INSTALLFILE_DEVPKG}" | while read A B; do
+ echo "${INSTALLDIR} debian/${PKGDEV}/${B}" >> "${execscript}"
+ echo "mv ${A} debian/${PKGDEV}/${B}" >> "${execscript}"
+done
+
+cat "${execscript}"
+
+# check the syntax of the control file.
+CHECK_ERROR=false
+
+check_line "${PKGDEV}" "Provides:.*${PK_LOWER}-dev"
+check_line "${PKGDEV}" "Conflicts:.*${PK_LOWER}-dev"
+check_line "${PKGSHL}" "Section: libs"
+if [ -n "${SUFFIX}" ]; then
+ check_line "${PKGSHL}" "Conflicts: ${SONAMEPKGNAME}"
+fi
+if [ -n "${TRANSITIONSUFFIX}" ]; then
+ check_line "${PKGSHL}" "Conflicts: ${SONAMEPKGNAME}${SUFFIX}"
+fi
+check_line "${PKGDEV}" "Section: \(devel\|libdevel\)"
+check_line "${PKGDEV}" "Depends:.*${PKGSHL}"
+check_line "${PKGSHL}" "Depends:.*[$]{shlibs:Depends}"
+
+if [ "${CHECK_ERROR}" = "true" ]; then
+ echo "Error occurred, aborting" >&2
+ exit 1
+fi
+
+if [ "${DOIT}" = "yes" ]; then
+ sh "${execscript}"
+else
+ echo "Dry-run. If you are satisfied, run with --commit"
+ exit 2
+fi
+rm -f "${execscript}" "${INSTALLFILE_DEVPKG}"" ${INSTALLFILE_SHLPKG}"
+
+exit 0
Property changes on: trunk/packages/muscle/branches/libmuscle/debian/d-shlibmove
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/muscle/branches/libmuscle/debian/get-orig-source
===================================================================
--- trunk/packages/muscle/branches/libmuscle/debian/get-orig-source (rev 0)
+++ trunk/packages/muscle/branches/libmuscle/debian/get-orig-source 2008-04-29 16:10:30 UTC (rev 1814)
@@ -0,0 +1,49 @@
+#!/bin/sh -e
+set -x
+
+URL="http://gel.ahabs.wisc.edu/mauve/source/snapshots/"
+NAME=libmuscle
+UVERSION=snapshot
+DVERSION=3.7
+UPSTREAMTAR=muscle-"$UVERSION".tar.gz
+UPSTREAMDIR=muscle
+
+# To rebuild the new upstream tarball you need these
+# packages installed. This will be checked later on.
+# The rationale behind this dependency is that the
+# script should work for later upstream releases as well
+# and thus a simple patch for Makefile.am and
+# configure.in would not work
+BUILDTARBALLDEPENDS="autoconf automake libtool"
+# Also these build-dependencies are needed to be installed to
+# run ./configure which is a precondition for "make dist"
+BUILDDEPS=""
+missingdepends=`dpkg -l ${BUILDTARBALLDEPENDS} ${BUILDDEPS} | \
+ grep -v -e "^ii" -e "^|" -e "^++" -e "^ " -e "^..[^[:space:]]" | \
+ sed 's/^[a-z][a-z][[:space:]]\+\([^[:space:]]\+\)[[:space:]]\+.*/\1/'`
+
+if [ "$missingdepends" != "" ] ; then
+ echo "Please install the following packages to rebuild the upstream source tarball:"
+ echo $missingdepends
+ exit -1
+fi
+
+mkdir -p ../tarballs
+cd ../tarballs
+
+if [ ! -f "$UPSTREAMTAR" ] ; then
+ wget "$URL"/"$UPSTREAMTAR"
+fi
+tar -xzf "$UPSTREAMTAR"
+
+cd "$UPSTREAMDIR"
+
+autogen.sh
+./configure
+make dist
+
+DISTTAR="libMUSCLE-1.0.0.tar.gz"
+DVERSION="${DVERSION}."`date +%Y%m%d`
+mv "$DISTTAR" ../"$NAME"_"$DVERSION".orig.tar.gz
+cd ..
+# rm -rf "$UPSTREAMDIR"
Property changes on: trunk/packages/muscle/branches/libmuscle/debian/get-orig-source
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/muscle/branches/libmuscle/debian/muscle.1
===================================================================
--- trunk/packages/muscle/branches/libmuscle/debian/muscle.1 (rev 0)
+++ trunk/packages/muscle/branches/libmuscle/debian/muscle.1 2008-04-29 16:10:30 UTC (rev 1814)
@@ -0,0 +1,135 @@
+.\" Title: MUSCLE
+.\" Author: Robert Elgar
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 02/06/2008
+.\" Manual: Muscle Manual
+.\" Source: muscle 3.7
+.\"
+.TH "MUSCLE" "1" "02/06/2008" "muscle 3.7" "Muscle Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+muscle - Multiple Protein Sequence Alignment
+.SH "SYNOPSIS"
+.HP 7
+\fBmuscle\fR \fB\-in\ \fR\fB\fIinput\ file\ (fasta)\fR\fR [\fB\-out\ \fR\fB\fIoutput\ file\ (default\ fasta)\fR\fR] [\fB\-diags\fR] [\fB\-log\ \fR\fB\fIlog\ file\fR\fR] [\fB\-maxiters\ \fR\fB\fIn\fR\fR] [\fB\-maxhours\ \fR\fB\fIn\fR\fR] [\fB\-maxmb\ \fR\fB\fIm\fR\fR] [\fB\-html\fR] [\fB\-msf\fR] [\fB\-clw\fR] [\fB\-clwstrict\fR] [\fB\-log[a]\ \fR\fB\fIlogfile\fR\fR] [\fB\-quiet\fR] [\fB\-stable\fR] [\fB\-group\fR] [\fB\-version\fR]
+.SH "DESCRIPTION"
+.PP
+This manual page documents briefly the
+\fBmuscle\fR
+command\.
+.PP
+\fBmuscle\fR
+aligns protein sequences and is considered superior and faster than Clustal\ W\.
+.SH "OPTIONS"
+.PP
+\fB\-in \fR\fB\fIinput file\fR\fR
+.RS 4
+Path to FASTA formatted input file
+.RE
+.PP
+\fB\-out \fR\fB\fIoutput file\fR\fR
+.RS 4
+Path to output file, FASTA formatted by default
+.RE
+.PP
+\fB\-diags\fR
+.RS 4
+Find diagonals (faster for similar sequences)
+.RE
+.PP
+\fB\-maxiters \fR\fB\fIn\fR\fR
+.RS 4
+Maximum number of iterations (integer, default 16)
+.RE
+.PP
+\fB\-maxhours \fR\fB\fIn\fR\fR
+.RS 4
+Maximum time to iterate in hours (default no limit)
+.RE
+.PP
+\fB\-maxmb \fR\fB\fIm\fR\fR
+.RS 4
+Maximum memory to allocate in Mb (default 80% of RAM)
+.RE
+.PP
+\fB\-html\fR
+.RS 4
+Write output in HTML format (default FASTA)
+.RE
+.PP
+\fB\-msf\fR
+.RS 4
+Write output in MSF format (default FASTA)
+.RE
+.PP
+\fB\-clw\fR
+.RS 4
+Write output in Clustal\ W format (default FASTA)
+.RE
+.PP
+\fB\-clwstrict\fR
+.RS 4
+As \-clw, with \'CLUSTAL W (1\.81)\' header
+.RE
+.PP
+\fB\-log[a] \fR\fB\fIlogfile\fR\fR
+.RS 4
+Log to file (append if \-loga, overwrite if \-log)
+.RE
+.PP
+\fB\-quiet\fR
+.RS 4
+Do not write progress messages to stderr
+.RE
+.PP
+\fB\-stable\fR
+.RS 4
+Output sequences in input order (default is \-group)
+.RE
+.PP
+\fB\-group\fR
+.RS 4
+Group sequences by similarity (this is the default)
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+Display version information and exit
+.RE
+.SH "SEE ALSO"
+.PP
+
+\fBclustalw\fR(1),
+\fBseaview\fR(1),
+\fBt_coffee\fR(1)\.
+.SH "AUTHORS"
+.PP
+\fBRobert Elgar\fR
+.sp -1n
+.IP "" 4
+Wrote Muscle\.
+.PP
+\fBSteffen Moeller\fR <\&moeller at debian\.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage\.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Updated this manpage\.
+.SH "COPYRIGHT"
+Copyright \(co 2003, 2004 Steffen Moeller (manpage)
+.br
+Copyright \(co 2007, 2008 Charles Plessy (manpage)
+.br
+.PP
+Muscle is in the public domain, and therefore not subjected to copyright\.
+.PP
+This manual page was written by Steffen Moeller moeller at debian\.org for the
+Debian(TM)
+system (but may be used by others)\. Permission is granted to copy, distribute and/or modify this document as if it were in public domain\.
+.sp
Added: trunk/packages/muscle/branches/libmuscle/debian/muscle.1.xml
===================================================================
--- trunk/packages/muscle/branches/libmuscle/debian/muscle.1.xml (rev 0)
+++ trunk/packages/muscle/branches/libmuscle/debian/muscle.1.xml 2008-04-29 16:10:30 UTC (rev 1814)
@@ -0,0 +1,270 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<?xml-stylesheet type="text/xsl"
+ href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+ "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
+
+<!--
+
+Process this file with an XSLT processor: `xsltproc \
+-''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
+manpages/docbook.xsl manpage.dbk'. A manual page
+<package>.<section> will be generated. You may view the
+manual page with: nroff -man <package>.<section> | less'. A
+typical entry in a Makefile or Makefile.am is:
+
+DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
+manpages/docbook.xsl
+XP=xsltproc -''-nonet
+
+manpage.1: manpage.dbk
+ $(XP) $(DB2MAN) $<
+
+The xsltproc binary is found in the xsltproc package. The
+XSL files are in docbook-xsl. Please remember that if you
+create the nroff version in one of the debian/rules file
+targets (such as build), you will need to include xsltproc
+and docbook-xsl in your Build-Depends control field.
+
+-->
+
+ <!ENTITY dhfirstname "Steffen">
+ <!ENTITY dhsurname "Moeller">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "moeller at debian.org">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>MUSCLE</refentrytitle>">
+ <!ENTITY dhpackage "muscle">
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+ <!ENTITY dhrelease "3.7">
+ <!ENTITY dhtitle "Muscle Manual">
+]>
+
+<refentry>
+ <refentryinfo>
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <authorgroup>
+ <author>
+ <firstname>Robert</firstname>
+ <firstname>C.</firstname>
+ <surname>Elgar</surname>
+ <contrib>Wrote Muscle.</contrib>
+ </author>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Wrote this manpage.</contrib>
+ <address><email>&dhemail;</email></address>
+ </author>
+ <author>
+ <firstname>Charles</firstname>
+ <surname>Plessy</surname>
+ <contrib>Updated this manpage.</contrib>
+ <address><email>charles-debian-nospam at plessy.org</email></address>
+ </author>
+ </authorgroup>
+ <copyright>
+ <year>2003</year>
+ <year>2004</year>
+ <holder>&dhusername; (manpage)</holder>
+ </copyright>
+ <copyright>
+ <year>2007</year>
+ <year>2008</year>
+ <holder>Charles Plessy (manpage)</holder>
+ </copyright>
+ <legalnotice>
+ <para>
+ Muscle is in the public domain, and therefore not subjected to copyright.
+ </para>
+
+ <para>
+ This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document as if it were in public domain.
+ </para>
+ </legalnotice>
+ </refentryinfo>
+
+ <refmeta>
+ &dhucpackage;
+ &dhsection;
+ </refmeta>
+
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>Multiple Protein Sequence Alignment</refpurpose>
+ </refnamediv>
+
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="plain"><option>-in <replaceable>input file (fasta)</replaceable></option></arg>
+ <arg choice="opt"><option>-out <replaceable>output file (default fasta)</replaceable></option></arg>
+ <arg choice="opt"><option>-diags</option></arg>
+ <arg choice="opt"><option>-log <replaceable>log file</replaceable></option></arg>
+ <arg choice="opt"><option>-maxiters <replaceable>n</replaceable></option></arg>
+ <arg choice="opt"><option>-maxhours <replaceable>n</replaceable></option></arg>
+ <arg choice="opt"><option>-maxmb <replaceable>m</replaceable></option></arg>
+ <arg choice="opt"><option>-html</option></arg>
+ <arg choice="opt"><option>-msf</option></arg>
+ <arg choice="opt"><option>-clw</option></arg>
+ <arg choice="opt"><option>-clwstrict</option></arg>
+ <arg choice="opt"><option>-log[a] <replaceable>logfile</replaceable></option></arg>
+ <arg choice="opt"><option>-quiet</option></arg>
+ <arg choice="opt"><option>-stable</option></arg>
+ <arg choice="opt"><option>-group</option></arg>
+ <arg choice="opt"><option>-version</option></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+
+ <refsect1>
+ <title>DESCRIPTION</title>
+
+ <para>This manual page documents briefly the
+ <command>&dhpackage;</command> command.
+ </para>
+
+ <para><command>&dhpackage;</command> aligns protein sequences and is considered superior and faster than Clustal W.</para>
+ </refsect1>
+
+ <refsect1>
+ <title>OPTIONS</title>
+ <variablelist>
+ <varlistentry>
+ <term><option>-in <replaceable>input file</replaceable></option>
+ </term>
+ <listitem>
+ <para>Path to FASTA formatted input file
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-out <replaceable>output file</replaceable></option>
+ </term>
+ <listitem>
+ <para>Path to output file, FASTA formatted by default
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-diags</option>
+ </term>
+ <listitem>
+ <para>Find diagonals (faster for similar sequences)
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-maxiters <replaceable>n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Maximum number of iterations (integer, default 16)
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-maxhours <replaceable>n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Maximum time to iterate in hours (default no limit)
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-maxmb <replaceable>m</replaceable></option></term>
+ <listitem>
+ <para>Maximum memory to allocate in Mb (default 80% of RAM)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-html</option>
+ </term>
+ <listitem>
+ <para>Write output in HTML format (default FASTA)</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-msf</option>
+ </term>
+ <listitem>
+ <para>Write output in MSF format (default FASTA)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-clw</option>
+ </term>
+ <listitem>
+ <para>Write output in Clustal W format (default FASTA)</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-clwstrict</option>
+ </term>
+ <listitem>
+ <para>As -clw, with 'CLUSTAL W (1.81)' header</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-log[a] <replaceable>logfile</replaceable></option>
+ </term>
+ <listitem>
+ <para>Log to file (append if -loga, overwrite if -log)</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-quiet</option>
+ </term>
+ <listitem>
+ <para>Do not write progress messages to stderr</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-stable</option>
+ </term>
+ <listitem>
+ <para>Output sequences in input order (default is -group)</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-group</option>
+ </term>
+ <listitem>
+ <para>Group sequences by similarity (this is the default)</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-version</option>
+ </term>
+ <listitem>
+ <para>Display version information and exit</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para>
+ <citerefentry>
+ <refentrytitle>clustalw</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,
+
+ <citerefentry>
+ <refentrytitle>seaview</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,
+
+ <citerefentry>
+ <refentrytitle>t_coffee</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>.
+ </para>
+ </refsect1>
+</refentry>
Added: trunk/packages/muscle/branches/libmuscle/debian/muscle.install
===================================================================
--- trunk/packages/muscle/branches/libmuscle/debian/muscle.install (rev 0)
+++ trunk/packages/muscle/branches/libmuscle/debian/muscle.install 2008-04-29 16:10:30 UTC (rev 1814)
@@ -0,0 +1,2 @@
+libMUSCLE/muscle usr/bin
+
Added: trunk/packages/muscle/branches/libmuscle/debian/muscle.manpages
===================================================================
--- trunk/packages/muscle/branches/libmuscle/debian/muscle.manpages (rev 0)
+++ trunk/packages/muscle/branches/libmuscle/debian/muscle.manpages 2008-04-29 16:10:30 UTC (rev 1814)
@@ -0,0 +1 @@
+debian/muscle.1
Added: trunk/packages/muscle/branches/libmuscle/debian/rules
===================================================================
--- trunk/packages/muscle/branches/libmuscle/debian/rules (rev 0)
+++ trunk/packages/muscle/branches/libmuscle/debian/rules 2008-04-29 16:10:30 UTC (rev 1814)
@@ -0,0 +1,29 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/autotools.mk
+
+pkg=libmuscle
+name=libMUSCLE
+version=3.7
+
+common-binary-post-install-arch::
+ # Call d-shlibmove to comply with library packaging guide
+ d-devlibdeps debian/$(pkg)1-dev.substvars \
+ debian/tmp/usr/lib/$(name)-$(version).so
+ # /bin/sh debian/debug/
+ mv debian/tmp/usr/include/*/* debian/tmp/usr/include/
+ # cp -a doc/html/* debian/tmp/usr/share/doc/html
+ /bin/bash debian/d-shlibmove --commit \
+ --movedev "debian/tmp/usr/include/$(name)" usr/include/$(name)-$(version) \
+ --movedev "$(name)-$(version).pc" usr/share/pkgconfig \
+ debian/tmp/usr/lib/$(name)-$(version).so
+
+# --movedevdoc "debian/tmp/usr/share/doc/html/*" \
+
+get-orig-source:
+ . debian/get-orig-source
+
+clean::
+ rm -f debian/$(pkg)1-dev.substvars
Property changes on: trunk/packages/muscle/branches/libmuscle/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/muscle/branches/libmuscle/debian/watch
===================================================================
--- trunk/packages/muscle/branches/libmuscle/debian/watch (rev 0)
+++ trunk/packages/muscle/branches/libmuscle/debian/watch 2008-04-29 16:10:30 UTC (rev 1814)
@@ -0,0 +1,3 @@
+version=3
+
+http://gel.ahabs.wisc.edu/mauve/source/libGenome-(.*)\.tar\.gz
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