Author: tille Date: 2010-11-24 22:17:06 +0000 (Wed, 24 Nov 2010) New Revision: 5491
Added: trunk/packages/theseus/trunk/debian/patches/use_muscle_instead_of_clustalw.patch trunk/packages/theseus/trunk/debian/source/ trunk/packages/theseus/trunk/debian/source/format Modified: trunk/packages/theseus/trunk/debian/changelog trunk/packages/theseus/trunk/debian/control trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch trunk/packages/theseus/trunk/debian/patches/series trunk/packages/theseus/trunk/debian/theseus_align.1 Log: Adapt patches to new upstream version; Make sure muscle instead of non-free clustalw will be used as aligner and adjust dependency of muscle accordingly; source format 3 Modified: trunk/packages/theseus/trunk/debian/changelog =================================================================== --- trunk/packages/theseus/trunk/debian/changelog 2010-11-24 17:02:13 UTC (rev 5490) +++ trunk/packages/theseus/trunk/debian/changelog 2010-11-24 22:17:06 UTC (rev 5491) @@ -1,8 +1,15 @@ -theseus (1.5.5-1) UNRELEASED; urgency=low +theseus (1.5.5-1) unstable; urgency=low * New upstream version * Standards-Version: 3.9.1 (no changes needed) * Adapt debian/patches to new upstream version + * Source format 3.0 (quilt) + * debian/patches/use_muscle_instead_of_clustalw.patch: + The script thesaus_align says it would use muscle as align program + but it actually uses clustalw which is in non-free and thus we can + not recommend it. The patch makes muscle really the default + * Depends: muscle (instead of Suggests) + * debian/theseus_align.1: Better wording for muscle preference -- Andreas Tille <[email protected]> Wed, 24 Nov 2010 17:46:49 +0100 Modified: trunk/packages/theseus/trunk/debian/control =================================================================== --- trunk/packages/theseus/trunk/debian/control 2010-11-24 17:02:13 UTC (rev 5490) +++ trunk/packages/theseus/trunk/debian/control 2010-11-24 22:17:06 UTC (rev 5491) @@ -5,7 +5,7 @@ Uploaders: Morten Kjeldgaard <[email protected]>, Andreas Tille <[email protected]> DM-Upload-Allowed: yes -Build-Depends: debhelper (>= 7.1), quilt, libgsl0-dev, liblapack-dev, libtool +Build-Depends: debhelper (>= 7.1), quilt (>= 0.47), libgsl0-dev, liblapack-dev, libtool Standards-Version: 3.9.1 Homepage: http://www.theseus3d.org Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/theseus/trunk/ @@ -13,8 +13,8 @@ Package: theseus Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} -Suggests: muscle, clustlaw, mafft, t-coffee, kalign, dialign +Depends: ${shlibs:Depends}, ${misc:Depends}, muscle +Suggests: clustlaw, mafft, t-coffee, kalign, dialign Description: superimpose macromolecules using maximum likelihood Theseus is a program that simultaneously superimposes multiple macromolecular structures. Theseus finds the optimal solution to the Modified: trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch =================================================================== --- trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch 2010-11-24 17:02:13 UTC (rev 5490) +++ trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch 2010-11-24 22:17:06 UTC (rev 5491) @@ -2,9 +2,9 @@ Author: Cyril Brulebois <[email protected]>, Andreas Tille <[email protected]> Fixes: #542879 ---- theseus.orig/distfit.h -+++ theseus/distfit.h -@@ -713,7 +713,7 @@ +--- theseus_src.orig/distfit.h ++++ theseus_src/distfit.h +@@ -752,7 +752,7 @@ #ifndef LOGNORMAL_SEEN #define LOGNORMAL_SEEN @@ -13,7 +13,7 @@ extern double erf(double x); #endif -@@ -1446,7 +1446,7 @@ +@@ -1485,7 +1485,7 @@ #ifndef VONMISES_DIST_SEEN #define VONMISES_DIST_SEEN @@ -22,8 +22,8 @@ extern double jn(int n, double x); #endif ---- theseus.orig/theseus.h -+++ theseus/theseus.h +--- theseus_src.orig/theseus.h ++++ theseus_src/theseus.h @@ -51,7 +51,7 @@ #include <string.h> #include <stdio.h> Modified: trunk/packages/theseus/trunk/debian/patches/series =================================================================== --- trunk/packages/theseus/trunk/debian/patches/series 2010-11-24 17:02:13 UTC (rev 5490) +++ trunk/packages/theseus/trunk/debian/patches/series 2010-11-24 22:17:06 UTC (rev 5491) @@ -2,3 +2,4 @@ 200-make.inc.patch 99-theseus_align.sh.patch 10_kbsd.patch +use_muscle_instead_of_clustalw.patch Added: trunk/packages/theseus/trunk/debian/patches/use_muscle_instead_of_clustalw.patch =================================================================== --- trunk/packages/theseus/trunk/debian/patches/use_muscle_instead_of_clustalw.patch (rev 0) +++ trunk/packages/theseus/trunk/debian/patches/use_muscle_instead_of_clustalw.patch 2010-11-24 22:17:06 UTC (rev 5491) @@ -0,0 +1,29 @@ +Description: The script thesaus_align says it would use muscle as align program + but it actually uses clustalw which is in non-free and thus we can + not recommend it. The patch makes muscle really the default +Author: Andreas Tille <[email protected]> + +--- theseus_src.orig/theseus_align ++++ theseus_src/theseus_align +@@ -50,8 +50,8 @@ + alignmentfile="theseus.aln"; + + # for MUSCLE -- http://www.drive5.com/muscle/ +-#alignprog="/usr/bin/muscle"; +-#align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict"; ++alignprog="/usr/bin/muscle"; ++align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict"; + + # for PROBCONS -- http://probcons.stanford.edu/ + #alignprog="/usr/bin/probcons"; +@@ -59,8 +59,8 @@ + #echo $align_cmd + + # for CLUSTALW -- ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ +-alignprog="/usr/bin/clustalw"; +-align_cmd="${alignprog} -infile=${fastafile} -outfile=${alignmentfile}"; ++# alignprog="/usr/bin/clustalw"; ++# align_cmd="${alignprog} -infile=${fastafile} -outfile=${alignmentfile}"; + + # for MAFFT -- http://www.biophys.kyoto-u.ac.jp/%7Ekatoh/programs/align/mafft/ + #alignprog="/usr/bin/mafft"; Added: trunk/packages/theseus/trunk/debian/source/format =================================================================== --- trunk/packages/theseus/trunk/debian/source/format (rev 0) +++ trunk/packages/theseus/trunk/debian/source/format 2010-11-24 22:17:06 UTC (rev 5491) @@ -0,0 +1 @@ +3.0 (quilt) Modified: trunk/packages/theseus/trunk/debian/theseus_align.1 =================================================================== --- trunk/packages/theseus/trunk/debian/theseus_align.1 2010-11-24 17:02:13 UTC (rev 5490) +++ trunk/packages/theseus/trunk/debian/theseus_align.1 2010-11-24 22:17:06 UTC (rev 5491) @@ -39,12 +39,11 @@ that you supply. .P Second, these sequences are aligned using the multiple sequence alignment -program of your choice. The script is easily modified for CLUSTALW, +program of your choice. The script can easily be modified for CLUSTALW, T_COFFEE, KALIGN, DIALIGN2, or MAFFT. Any multiple sequence alignment program can be used, as long as it can generate clustal-formatted files. However, I highly recommend Bob Edgar's MUSCLE program for both its -speed and accuracy. It is easy to install using either precompiled binaries -or by compiling from scratch: http://www.drive5.com/muscle/ +speed and accuracy. (For more info see http://www.drive5.com/muscle/ .) .P Third, \fBtheseus\fR performs a superposition of the structures using the sequence alignment as a guide. _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
