[med-svn] r16749 - in trunk/packages/staden/trunk/debian: . bash_completion bin patches
Andreas Tille
tille at moszumanska.debian.org
Mon Apr 21 20:38:19 UTC 2014
Author: tille
Date: 2014-04-21 20:38:19 +0000 (Mon, 21 Apr 2014)
New Revision: 16749
Added:
trunk/packages/staden/trunk/debian/bash_completion/
trunk/packages/staden/trunk/debian/bash_completion/staden
trunk/packages/staden/trunk/debian/bin/
trunk/packages/staden/trunk/debian/bin/staden
trunk/packages/staden/trunk/debian/patches/enable_setting_stadenroot.patch
trunk/packages/staden/trunk/debian/staden.links
Modified:
trunk/packages/staden/trunk/debian/changelog
trunk/packages/staden/trunk/debian/copyright
trunk/packages/staden/trunk/debian/patches/series
trunk/packages/staden/trunk/debian/staden.install
Log:
wrapper script for staden to provide access to all binaries, main binaries available via additional symlink
Added: trunk/packages/staden/trunk/debian/bash_completion/staden
===================================================================
--- trunk/packages/staden/trunk/debian/bash_completion/staden (rev 0)
+++ trunk/packages/staden/trunk/debian/bash_completion/staden 2014-04-21 20:38:19 UTC (rev 16749)
@@ -0,0 +1,47 @@
+_staden()
+{
+ local cur prev opts
+ COMPREPLY=()
+ cur="${COMP_WORDS[COMP_CWORD]}"
+ prev="${COMP_WORDS[COMP_CWORD-1]}"
+
+ opts="alfsplit
+ copy_db
+ copy_reads
+ create_emboss_files
+ eba
+ find_renz
+ gap4
+ gap5
+ gap5_cmd
+ getABIcomment
+ getABIdate
+ getABIfield
+ getABISampleName
+ get_scf_field
+ hetins
+ init_exp
+ make_weights
+ mutscan
+ polyA_clip
+ prefinish
+ pregap4
+ qclip
+ screen_seq
+ spin
+ staden_convert
+ stash
+ stops
+ tg_index
+ tracediff
+ trev
+ vector_clip"
+
+ case $prev in
+ staden)
+ COMPREPLY=( $(compgen -f -W "${opts}" -- "$cur") )
+ ;;
+ esac
+ return 0
+}
+complete -F _staden -o default staden
Added: trunk/packages/staden/trunk/debian/bin/staden
===================================================================
--- trunk/packages/staden/trunk/debian/bin/staden (rev 0)
+++ trunk/packages/staden/trunk/debian/bin/staden 2014-04-21 20:38:19 UTC (rev 16749)
@@ -0,0 +1,25 @@
+#!/bin/sh
+
+BINDIR=/usr/lib/staden/bin
+export STADENROOT=/usr
+
+if [ $# -lt 1 ] ; then
+ echo "Usage: $0 <program>" 1>&2
+ echo " Existing programs are:"
+ ls ${BINDIR}
+ exit 1
+fi
+
+WRAPPER=$0
+PROGRAM=$1
+shift
+ARGS=$*
+
+if [ -x ${BINDIR}/${PROGRAM} ]; then
+ exec ${BINDIR}/${PROGRAM} ${ARGS}
+else
+ echo "Usage: ${PROGRAM} does not exist in Staden"
+ echo " Existing programs are:"
+ ls ${BINDIR}
+ exit 1
+fi
Modified: trunk/packages/staden/trunk/debian/changelog
===================================================================
--- trunk/packages/staden/trunk/debian/changelog 2014-04-21 17:02:28 UTC (rev 16748)
+++ trunk/packages/staden/trunk/debian/changelog 2014-04-21 20:38:19 UTC (rev 16749)
@@ -1,4 +1,4 @@
-staden (2.0.0~b10-1) UNRELEASED; urgency=low
+staden (2.0.0+b10-1) UNRELEASED; urgency=low
FIXME: TODO
it seems gap[45], pregap4, spin (not sure about trev) are the main
@@ -21,8 +21,10 @@
Jonas Smedegaard
* Fix several lintian issues
* fix watch file
+ * wrapper script for staden to provide access to all binaries,
+ main binaries available via additional symlink
- -- Andreas Tille <tille at debian.org> Mon, 20 Jan 2014 11:21:17 +0100
+ -- Andreas Tille <tille at debian.org> Mon, 21 Apr 2014 22:34:28 +0200
staden (2.0.0b9-0biolinux4) precise; urgency=low
Modified: trunk/packages/staden/trunk/debian/copyright
===================================================================
--- trunk/packages/staden/trunk/debian/copyright 2014-04-21 17:02:28 UTC (rev 16748)
+++ trunk/packages/staden/trunk/debian/copyright 2014-04-21 20:38:19 UTC (rev 16749)
@@ -87,3 +87,31 @@
Copyright: 2013 Tim Booth <tbooth at ceh.ac.uk>
2013-2014 Andreas Tille <tille at debian.org>
License: BSD-like
+
+License: BSD-like
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ .
+ Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ .
+ Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
+ MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or
+ promote products derived from this software without specific prior written
+ permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
Added: trunk/packages/staden/trunk/debian/patches/enable_setting_stadenroot.patch
===================================================================
--- trunk/packages/staden/trunk/debian/patches/enable_setting_stadenroot.patch (rev 0)
+++ trunk/packages/staden/trunk/debian/patches/enable_setting_stadenroot.patch 2014-04-21 20:38:19 UTC (rev 16749)
@@ -0,0 +1,76 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 21 Apr 2014 22:34:28 +0200
+Description: Make sure the main scripts will find the staden.profile
+ file when installed to the location where the wrapper will seek for
+ the scripts
+
+--- staden-2.0.0b10-src.orig/gap5/gap5.in
++++ staden-2.0.0b10-src/gap5/gap5.in
+@@ -67,7 +67,10 @@
+ echo $dir
+ }
+
+-STADENROOT=`find_dir $0`/..; export STADENROOT
++STADENROOT=${STADENROOT:-`find_dir $0`/..}; export STADENROOT
++if [ ! -f "$STADENROOT"/share/staden/staden.profile ] ; then
++ STADENROOT=/usr
++fi
+ STADEN_PREPEND=1; export STADEN_PREPEND
+ . "$STADENROOT"/share/staden/staden.profile
+
+--- staden-2.0.0b10-src.orig/gap4/gap4.in
++++ staden-2.0.0b10-src/gap4/gap4.in
+@@ -67,7 +67,10 @@
+ echo $dir
+ }
+
+-STADENROOT=`find_dir $0`/..; export STADENROOT
++STADENROOT=${STADENROOT:-`find_dir $0`/..}; export STADENROOT
++if [ ! -f "$STADENROOT"/share/staden/staden.profile ] ; then
++ STADENROOT=/usr
++fi
+ STADEN_PREPEND=1; export STADEN_PREPEND
+ . "$STADENROOT"/share/staden/staden.profile
+
+--- staden-2.0.0b10-src.orig/pregap4/pregap4.in
++++ staden-2.0.0b10-src/pregap4/pregap4.in
+@@ -67,7 +67,10 @@
+ echo $dir
+ }
+
+-STADENROOT=`find_dir $0`/..; export STADENROOT
++STADENROOT=${STADENROOT:-`find_dir $0`/..}; export STADENROOT
++if [ ! -f "$STADENROOT"/share/staden/staden.profile ] ; then
++ STADENROOT=/usr
++fi
+ STADEN_PREPEND=1; export STADEN_PREPEND
+ . "$STADENROOT"/share/staden/staden.profile
+
+--- staden-2.0.0b10-src.orig/spin/spin.in
++++ staden-2.0.0b10-src/spin/spin.in
+@@ -67,7 +67,10 @@
+ echo $dir
+ }
+
+-STADENROOT=`find_dir $0`/..; export STADENROOT
++STADENROOT=${STADENROOT:-`find_dir $0`/..}; export STADENROOT
++if [ ! -f "$STADENROOT"/share/staden/staden.profile ] ; then
++ STADENROOT=/usr
++fi
+ STADEN_PREPEND=1; export STADEN_PREPEND
+ . "$STADENROOT"/share/staden/staden.profile
+
+--- staden-2.0.0b10-src.orig/trev/trev.in
++++ staden-2.0.0b10-src/trev/trev.in
+@@ -70,7 +70,10 @@
+ #
+ # Run it!
+ #
+-STADENROOT=`find_dir $0`/..; export STADENROOT
++STADENROOT=${STADENROOT:-`find_dir $0`/..}; export STADENROOT
++if [ ! -f "$STADENROOT"/share/staden/staden.profile ] ; then
++ STADENROOT=/usr
++fi
+ STADEN_PREPEND=1; export STADEN_PREPEND
+ . "$STADENROOT"/share/staden/staden.profile
+
Modified: trunk/packages/staden/trunk/debian/patches/series
===================================================================
--- trunk/packages/staden/trunk/debian/patches/series 2014-04-21 17:02:28 UTC (rev 16748)
+++ trunk/packages/staden/trunk/debian/patches/series 2014-04-21 20:38:19 UTC (rev 16749)
@@ -5,3 +5,4 @@
fix_tcl_path.patch
fix_awk.patch
# delete_rpath_from_configure.patch
+enable_setting_stadenroot.patch
Modified: trunk/packages/staden/trunk/debian/staden.install
===================================================================
--- trunk/packages/staden/trunk/debian/staden.install 2014-04-21 17:02:28 UTC (rev 16748)
+++ trunk/packages/staden/trunk/debian/staden.install 2014-04-21 20:38:19 UTC (rev 16749)
@@ -1,5 +1,7 @@
usr/lib
-usr/bin
+usr/bin usr/lib/staden
usr/share/man
-debian/icons/*.desktop /usr/share/applications
-debian/icons/*.svg /usr/share/staden
+debian/icons/*.desktop usr/share/applications
+debian/icons/*.svg usr/share/staden
+debian/bin usr
+debian/bash_completion/* etc/bash_completion.d
\ No newline at end of file
Added: trunk/packages/staden/trunk/debian/staden.links
===================================================================
--- trunk/packages/staden/trunk/debian/staden.links (rev 0)
+++ trunk/packages/staden/trunk/debian/staden.links 2014-04-21 20:38:19 UTC (rev 16749)
@@ -0,0 +1,5 @@
+usr/lib/staden/bin/gap4 usr/bin/gap4
+usr/lib/staden/bin/gap5 usr/bin/gap5
+usr/lib/staden/bin/pregap4 usr/bin/pregap4
+usr/lib/staden/bin/spin usr/bin/spin
+usr/lib/staden/bin/trev usr/bin/trev
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