[med-svn] r5834 - trunk/packages/tm-align/trunk/debian
Andreas Tille
tille at alioth.debian.org
Sun Jan 30 21:51:13 UTC 2011
Author: tille
Date: 2011-01-30 21:51:11 +0000 (Sun, 30 Jan 2011)
New Revision: 5834
Added:
trunk/packages/tm-align/trunk/debian/get-orig-source
Modified:
trunk/packages/tm-align/trunk/debian/changelog
trunk/packages/tm-align/trunk/debian/compat
trunk/packages/tm-align/trunk/debian/control
trunk/packages/tm-align/trunk/debian/rules
Log:
Added (working) get-orig-source, cleaned up changelog which should not be that verbose for not yet uploaded packages, debhelper 7
Modified: trunk/packages/tm-align/trunk/debian/changelog
===================================================================
--- trunk/packages/tm-align/trunk/debian/changelog 2011-01-30 21:03:03 UTC (rev 5833)
+++ trunk/packages/tm-align/trunk/debian/changelog 2011-01-30 21:51:11 UTC (rev 5834)
@@ -1,43 +1,5 @@
-tm-align (20110124-1) unstable; urgency=low
+tm-align (20110130-1) unstable; urgency=low
- * New upstream version
- - 2005/06/01: A small bug of two-point superposition was fixed.
- - 2005/10/19: the program was reformed so that the alignment results
- are not dependent on the specific compilers.
- - 2006/06/20: select 'A' if there is altLoc when reading PDB file.
- - 2007/02/27: rotation matrix from Chain-1 to Chain-2 was added.
- - 2007/04/18: added options with TM-score normalized by average
- length, shorter length, or longer length of two
- structures.
- - 2007/05/23: added additional output file 'TM.sup_all' for showing
- all atoms while 'TM.sup' is only for aligned atoms
- - 2007/09/19: added a new feature alignment to deal with the problem
- of aligning fractional structures (e.g. protein
- interfaces).
- - 2007/10/16: A bug for irregular bond-length models was fixed.
- - 2009/03/14: A new initial alignment was added and previous initial
- alignments are further enhanced. This change increased
- accuracy by 4% but increases CPU cost by 40%.
- - 2009/08/20: A bug for asymmetry alignment result was fixed.
- - 2010/08/02: A new RMSD matrix was used to remove obsolete
- statements. Staled subroutines were deleted.
- - 2011/01/03: The length of pdb file names were extended to 500
- - 2011/01/24: Fixed a bug on output file name created on 2011/01/03
- * Tweaked get-orig-source in rules to spot version in upstream file
-
- * New standards version 3.9.4
-
- -- Tim Booth <tbooth at ceh.ac.uk> Sun, 30 Jan 2011 13:34:53 +0000
-
-tm-align (20050601-2) UNRELEASED; urgency=low
-
- * Updated to Standards-Version 3.7.3 (no changes needed)
-
- -- David Paleino <d.paleino at gmail.com> Wed, 06 Feb 2008 13:11:58 +0100
-
-tm-align (20050601-1) unstable; urgency=low
-
* Initial release (Closes: #447505)
- -- Steffen Moeller <moeller at debian.org> Sun, 21 Oct 2007 17:11:53 +0200
-
+ -- Andreas Tille <tille at debian.org> Sun, 30 Jan 2011 22:49:21 +0100
Modified: trunk/packages/tm-align/trunk/debian/compat
===================================================================
--- trunk/packages/tm-align/trunk/debian/compat 2011-01-30 21:03:03 UTC (rev 5833)
+++ trunk/packages/tm-align/trunk/debian/compat 2011-01-30 21:51:11 UTC (rev 5834)
@@ -1 +1 @@
-5
+7
Modified: trunk/packages/tm-align/trunk/debian/control
===================================================================
--- trunk/packages/tm-align/trunk/debian/control 2011-01-30 21:03:03 UTC (rev 5833)
+++ trunk/packages/tm-align/trunk/debian/control 2011-01-30 21:51:11 UTC (rev 5834)
@@ -3,9 +3,11 @@
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
-Uploaders: Steffen Moeller <moeller at debian.org>, Tim Booth <tbooth at ceh.ac.uk>
-Build-Depends: debhelper (>= 5), gfortran
-Standards-Version: 3.9.4
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Tim Booth <tbooth at ceh.ac.uk>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7), gfortran
+Standards-Version: 3.9.1
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/tm-align/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/tm-align/trunk/
Homepage: http://zhang.bioinformatics.ku.edu/TM-align/
Added: trunk/packages/tm-align/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/tm-align/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/tm-align/trunk/debian/get-orig-source 2011-01-30 21:51:11 UTC (rev 5834)
@@ -0,0 +1,20 @@
+#!/bin/sh
+tmpdir=tm-align-tmp
+srcfile=TMalign.f
+[ -d "$tmpdir" ] && rm -rf "$tmpdir"
+mkdir "$tmpdir"
+wget -N -q http://zhanglab.ccmb.med.umich.edu/TM-align/"$srcfile" --output-document="$tmpdir"/"$srcfile"
+if [ ! -s "$tmpdir"/"$srcfile" ] ; then
+ echo "Failed to download $srcfile from http://zhanglab.ccmb.med.umich.edu/TM-align/"
+ exit -1
+fi
+version=`egrep '\* [0-9]{4}/[0-9]{2}/[0-9]{2}: ' "$tmpdir"/"$srcfile" | tail -n 1 | cut -f 1 -d : | sed 's/[* /]//g'`
+if [ "$version" = "" ] ; then
+ echo "Failed to obtain version number from $tmpdir/$srcfile. Giving up."
+ exit -1
+fi
+newname="tm-align-${version}"
+[ -d "$newname" ] && rm -rf $newname
+mv $tmpdir $newname
+GZIP="--best --no-name" tar czvf tm-align_${version}.orig.tar.gz $newname
+[ -d "$newname" ] && rm -rf $newname
Modified: trunk/packages/tm-align/trunk/debian/rules
===================================================================
--- trunk/packages/tm-align/trunk/debian/rules 2011-01-30 21:03:03 UTC (rev 5833)
+++ trunk/packages/tm-align/trunk/debian/rules 2011-01-30 21:51:11 UTC (rev 5834)
@@ -64,13 +64,6 @@
binary: binary-arch
get-orig-source:
- mkdir tm-align-tmp
- ( cd tm-align-tmp && wget http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.f ) ; \
- version=`egrep '\* [0-9]{4}/[0-9]{2}/[0-9]{2}: ' tm-align-20050601/TMalign.f | tail -n 1 | cut -f 1 -d : | sed 's/[* /]//g'` ; \
- newname="tm-align-$$version" ;\
- [ -d "$$newname" ] && rm -rf $$newname ; \
- mv tm-align-tmp $$newname ; \
- tar czvf tm-align_$$version.orig.tar.gz $$newname ; \
- [ -d "$$newname" ] && rm -rf $$newname
+ . debian/get-orig-source
.PHONY: build clean binary-indep binary-arch binary install configure
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