Author: tille Date: 2013-08-02 12:34:33 +0000 (Fri, 02 Aug 2013) New Revision: 14317
Added: trunk/packages/tm-align/trunk/ trunk/packages/tm-align/trunk/debian/ trunk/packages/tm-align/trunk/debian/README.Debian trunk/packages/tm-align/trunk/debian/TMalign.1 trunk/packages/tm-align/trunk/debian/TMscore.1 trunk/packages/tm-align/trunk/debian/TMscore.pod 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/copyright trunk/packages/tm-align/trunk/debian/get-orig-source trunk/packages/tm-align/trunk/debian/install trunk/packages/tm-align/trunk/debian/manpages trunk/packages/tm-align/trunk/debian/rules trunk/packages/tm-align/trunk/debian/source/ trunk/packages/tm-align/trunk/debian/source/format trunk/packages/tm-align/trunk/debian/upstream trunk/packages/tm-align/trunk/debian/watch Log: Commit currently release state of tm-align because unable to restore old version via svn checkout -r 11505 svn+ssh://svn.debian.org/svn/debian-med/trunk/packages/tm-align Added: trunk/packages/tm-align/trunk/debian/README.Debian =================================================================== --- trunk/packages/tm-align/trunk/debian/README.Debian (rev 0) +++ trunk/packages/tm-align/trunk/debian/README.Debian 2013-08-02 12:34:33 UTC (rev 14317) @@ -0,0 +1,38 @@ +README.Debian for TMalign and TMScore +------------------------------------- + +The homepage of TM-align (http://zhanglab.ccmb.med.umich.edu/TM-align/) says: + + TM-align is a computer algorithm for protein structure alignment using + dynamic programming and TM-score rotation matrix. An optimal alignment + between two proteins, as well as the TM-score, will be reported for each + comparison. The value of TM-score lies in (0,1]. In general, a + comparison of TM-score < 0.2 indicates that there is no similarity + between two structures; a TM-score > 0.5 means the structures share the + same fold. + +The homepage of TM-score (http://zhanglab.ccmb.med.umich.edu/TM-score/) says: + + TM-score is an algorithm to calculate the similarity of topologies of + two protein structures. It can be exploited to quantitatively access the + quality of protein structure predictions relative to native. Because + TM-score weights the close matches stronger than the distant matches, + TM-score is more sensitive than root-mean-square deviation (RMSD) (An + illustative example can be found from here). A single score between + (0,1] is assigned to each comparison. Based on statistics, if a + template/model has a TM-score around or below 0.17, it means the + prediction is nothing more than a random selection from PDB library. + +The difference between both programs is explained as follows: + + What is the difference between TM-score and TM-align? The TM-score + program is to compare two models based on their given and known residue + equivalency. It is usually NOT applied to compare two proteins of + different sequences. The TM-align is a structural alignment program for + comparing two proteins whose sequences can be different. The TM-align + will first find the best equivalent residues of two proteins based on + the structure similarity and then output a TM-score. The TM-score values + in both programs have the same definition. + + -- Andreas Tille <[email protected]> Sun, 30 Jan 2011 22:49:21 +0100 + Added: trunk/packages/tm-align/trunk/debian/TMalign.1 =================================================================== --- trunk/packages/tm-align/trunk/debian/TMalign.1 (rev 0) +++ trunk/packages/tm-align/trunk/debian/TMalign.1 2013-08-02 12:34:33 UTC (rev 14317) @@ -0,0 +1,75 @@ +.\" Hey, EMACS: -*- nroff -*- +.\" First parameter, NAME, should be all caps +.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection +.\" other parameters are allowed: see man(7), man(1) +.TH TMALIGN 1 "October 21, 2007" +.\" Please adjust this date whenever revising the manpage. +.\" +.\" Some roff macros, for reference: +.\" .nh disable hyphenation +.\" .hy enable hyphenation +.\" .ad l left justify +.\" .ad b justify to both left and right margins +.\" .nf disable filling +.\" .fi enable filling +.\" .br insert line break +.\" .sp <n> insert n+1 empty lines +.\" for manpage-specific macros, see man(7) + + +.SH NAME +TMalign \- protein structure alignment +.SH SYNOPSIS +.B TMalign +.RI structure.pdb target.pdb [ options ] + +.SH DESCRIPTION + +TMalign performs a structural alignment of proteins. The alignment is scored by +the TM-score algorithm. + +.PP +.\" TeX users may be more comfortable with the \fB<whatever>\fP and +.\" \fI<whatever>\fP escape sequences to invode bold face and italics, +.\" respectively. +.SH OPTIONS +When started with no options, a summary of commands is given. With two protein structures presented as arguments, the TM-score uses the length of the second protein to be normalised. +The final structural alignment is invariant to any of the options below. +.TP +.B -L +.IR number +normalises TM-score by an assigned length (in aa) +.TP +.B -a +normalises TM-score by the average length of the two structures +.TP +.B -b +normalises TM-score by the length of the shorter of the two structures +.TP +.BR -c +normalises TM-score by the length of the longer of the two structures + +.TP +.BR -o +.IR filename +Run TM-align and output the superposition to 'filename.sup' and 'filename.sup_all'. +The output files serve as scripts to the program +.IR rasmol. +To view the superimposed structures of the aligned regions call + 'rasmol -script TM.sup' To view the superimposed structures of all regions + 'rasmol -script TM.sup_all'. + +.SH SEE ALSO +.BR http://zhang.bioinformatics.ku.edu/TM-align/, +.BR rasmol(1) +.br +When using this proram and for more detailed information, please +refer to the publication in +.IR Nucleic Acids Res. +(2005) Volume 33 page 2303ff. by Zhang and Skolnick. + +.SH AUTHOR +tm-align was written by Zhang and Skolnick. +.PP +This manual page was written by Steffen Moeller <[email protected]>, +for the Debian project (but may be used by others). Added: trunk/packages/tm-align/trunk/debian/TMscore.1 =================================================================== --- trunk/packages/tm-align/trunk/debian/TMscore.1 (rev 0) +++ trunk/packages/tm-align/trunk/debian/TMscore.1 2013-08-02 12:34:33 UTC (rev 14317) @@ -0,0 +1,182 @@ +.\" Automatically generated by Pod::Man 2.22 (Pod::Simple 3.07) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. Capital omega is used to do unbreakable dashes and +.\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, +.\" nothing in troff, for use with C<>. +.tr \(*W- +.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' +.ie n \{\ +. ds -- \(*W- +. ds PI pi +. if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch +. if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch +. ds L" "" +. ds R" "" +. ds C` "" +. ds C' "" +'br\} +.el\{\ +. ds -- \|\(em\| +. ds PI \(*p +. ds L" `` +. ds R" '' +'br\} +.\" +.\" Escape single quotes in literal strings from groff's Unicode transform. +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" +.\" If the F register is turned on, we'll generate index entries on stderr for +.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index +.\" entries marked with X<> in POD. Of course, you'll have to process the +.\" output yourself in some meaningful fashion. +.ie \nF \{\ +. de IX +. tm Index:\\$1\t\\n%\t"\\$2" +.. +. nr % 0 +. rr F +.\} +.el \{\ +. de IX +.. +.\} +.\" +.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2). +.\" Fear. Run. Save yourself. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +TM\-score \- an algorithm to calculate the similarity of topologies of two protein structures +.SH "VERSION" +.IX Header "VERSION" +This documentation refers to TM-score version released on 2011/01/30 +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +1. Run TM-score to compare 'model' and 'native': +.PP +.Vb 1 +\& TMscore model native +.Ve +.PP +2. Run TM-score with an assigned d0, e.g. 5 Angstroms: +.PP +.Vb 1 +\& TMscore model native \-d 5 +.Ve +.PP +3. Run TM-score with superposition output, e.g. '\s-1TM\s0.sup', and view in Rasmol: +.PP +.Vb 2 +\& TMscore model native \-o TM.sup +\& rasmol \-script TM.sup +.Ve +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +This program is to compare two protein structures and identify the +best superposition that has the highest TM-score. Input structures +must be in the \s-1PDB\s0 format. By default, TM-score is normalized by +the second protein. Users can obtain a brief instruction by simply +running the program without arguments. +.SH "OPTIONS" +.IX Header "OPTIONS" +.RS 4 +\&\fB\-o\fR filename.sup Outputs the superposition to the specified file, + suitable for use in rasmol. +.Sp +\&\fB\-d\fR value Sets d0 to the specified number of angstroms. +.RE +.SH "SEE ALSO" +.IX Header "SEE ALSO" +TMalign, rasmol +.PP +When using this proram and for more detailed information, please refer to the publication in NucleicAcidsRes. +(2005) Volume 33 page 2303ff. by Zhang and Skolnick. +.SH "AUTHOR" +.IX Header "AUTHOR" +For comments/suggestions,please contact email: [email protected]. +.PP +This manpage was compiled by Tim Booth ([email protected]) Added: trunk/packages/tm-align/trunk/debian/TMscore.pod =================================================================== --- trunk/packages/tm-align/trunk/debian/TMscore.pod (rev 0) +++ trunk/packages/tm-align/trunk/debian/TMscore.pod 2013-08-02 12:34:33 UTC (rev 14317) @@ -0,0 +1,74 @@ +# +#=============================================================================== +# +# FILE: TMscore.pod +# +# DESCRIPTION: A POD-manpage for TMscore +# +# AUTHOR: Y. Zhang and J. Skolnick +# COMPANY: Zhang Lab University of Michigan +# CREATED: 03/02/11 14:18:17 GMT +# REVISION: --- +#=============================================================================== + + +=head1 NAME + +TM-score - an algorithm to calculate the similarity of topologies of two protein structures + +=head1 VERSION + +This documentation refers to TM-score version released on 2011/01/30 + + +=head1 SYNOPSIS + +1. Run TM-score to compare 'model' and 'native': + + TMscore model native + +2. Run TM-score with an assigned d0, e.g. 5 Angstroms: + + TMscore model native -d 5 + +3. Run TM-score with superposition output, e.g. 'TM.sup', and view in Rasmol: + + TMscore model native -o TM.sup + rasmol -script TM.sup + +=head1 DESCRIPTION + +This program is to compare two protein structures and identify the +best superposition that has the highest TM-score. Input structures +must be in the PDB format. By default, TM-score is normalized by +the second protein. Users can obtain a brief instruction by simply +running the program without arguments. + +=head1 OPTIONS + +=over 4 + +B<-o> L<filename.sup> Outputs the superposition to the specified file, + suitable for use in rasmol. + +B<-d> L<value> Sets d0 to the specified number of angstroms. + +=back + +=head1 SEE ALSO + +L<TMalign>, L<rasmol> + +When using this proram and for more detailed information, please refer to the publication in NucleicAcidsRes. +(2005) Volume 33 page 2303ff. by Zhang and Skolnick. + +=head1 AUTHOR + +For comments/suggestions,please contact email: [email protected]. + +This manpage was compiled by Tim Booth ([email protected]) + +=cut + + + Added: trunk/packages/tm-align/trunk/debian/changelog =================================================================== --- trunk/packages/tm-align/trunk/debian/changelog (rev 0) +++ trunk/packages/tm-align/trunk/debian/changelog 2013-08-02 12:34:33 UTC (rev 14317) @@ -0,0 +1,91 @@ +tm-align (20120507-1) unstable; urgency=low + + * New upstream version + * debian/rules: Add hardening options + + -- Andreas Tille <[email protected]> Fri, 29 Jun 2012 18:30:36 +0200 + +tm-align (20120124-1) unstable; urgency=low + + [ Charles Plessy ] + * debian/upstream: renamed from upstream-metadata.yaml + + [ Andreas Tille ] + * New upstream version + * debian/upstream: + - Fixed typo (s/TITILE/TITLE/) + - Moved DOI+PMID to references + * debian/control: Standards-Version: 3.9.3 (no changes needed) + * debhelper 9 (control+compat) + * debian/changelog: DEP5 verified using + cme fix dpkg-copyright + + -- Andreas Tille <[email protected]> Thu, 08 Mar 2012 15:35:07 +0100 + +tm-align (20111012-1) unstable; urgency=low + + * New upstream release + * Enhances t-coffee + * Standards-Version: 3.9.2 (no changes needed) + * Debhelper 8 (control + compat) + * Fixed Vcs fields + + -- Andreas Tille <[email protected]> Fri, 21 Oct 2011 10:00:04 +0200 + +tm-align (20110130-2) unstable; urgency=low + + * New upstream version (Closes: #447505) + - 2011/01/30: An open source license is attached to the program + * Reverting changelog to keep the history. + + -- Steffen Moeller <[email protected]> Sat, 05 Feb 2011 12:43:32 +0100 + +tm-align (20110130-1) UNRELEASED; urgency=low + + * Initial release. + + -- Andreas Tille <[email protected]> Sun, 30 Jan 2011 22:49:21 +0100 + +tm-align (20110124-1) UNRELEASED; 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 <[email protected]> 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 <[email protected]> Wed, 06 Feb 2008 13:11:58 +0100 + +tm-align (20050601-1) UNRELEASED; urgency=low + + * Initial packaging. + + -- Steffen Moeller <[email protected]> Sun, 21 Oct 2007 17:11:53 +0200 + Added: trunk/packages/tm-align/trunk/debian/compat =================================================================== --- trunk/packages/tm-align/trunk/debian/compat (rev 0) +++ trunk/packages/tm-align/trunk/debian/compat 2013-08-02 12:34:33 UTC (rev 14317) @@ -0,0 +1 @@ +9 Added: trunk/packages/tm-align/trunk/debian/control =================================================================== --- trunk/packages/tm-align/trunk/debian/control (rev 0) +++ trunk/packages/tm-align/trunk/debian/control 2013-08-02 12:34:33 UTC (rev 14317) @@ -0,0 +1,25 @@ +Source: tm-align +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Steffen Moeller <[email protected]>, + Tim Booth <[email protected]>, + Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 9), gfortran +Standards-Version: 3.9.3 +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/tm-align/trunk/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/tm-align/trunk/ +Homepage: http://zhang.bioinformatics.ku.edu/TM-align/ + +Package: tm-align +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Suggests: pymol, rasmol +Enhances: t-coffee +Description: structual alignment of proteins + TM-align is a computer algorithm for protein structure alignment using + dynamic programming. The scoring is performed by the TM-score rotation + matrix. This is similar to the RMSD in that unaligned portions of the + structure influence the scoring less than the more structurally conserved + regions. Added: trunk/packages/tm-align/trunk/debian/copyright =================================================================== --- trunk/packages/tm-align/trunk/debian/copyright (rev 0) +++ trunk/packages/tm-align/trunk/debian/copyright 2013-08-02 12:34:33 UTC (rev 14317) @@ -0,0 +1,22 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: TM-align +Upstream-Contact: Yang Zhang <[email protected]> +Source: http://zhanglab.ccmb.med.umich.edu/TM-align/ + +Files: * +Copyright: © 2005-2012 Yang Zhang, Jeffrey Skolnick +License: other + Permission to use, copy, modify, and distribute this program for + any purpose, with or without fee, is hereby granted, provided that + the notices on the head, the reference information, and this + copyright notice appear in all copies or substantial portions of + the Software. It is provided "as is" without express or implied + warranty. + +Files: debian/* +Copyright: © 2011 Tim Booth <[email protected]>, + © 2011-2012 Andreas Tille <[email protected]> +License: GPL + The Debian packaging is licensed under the GPL, see + `/usr/share/common-licenses/GPL'. + 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 2013-08-02 12:34:33 UTC (rev 14317) @@ -0,0 +1,31 @@ +#!/bin/sh + +# bail out with the first problem +set -e + +# script to download and repack source package of TMalign which strips the binaries from upstream tarball + +PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` +VERSION=`uscan --verbose --force-download | \ + grep "Newest version on remote site is .* local version is .*" | \ + head -n 1 | \ + sed "s/Newest version on remote site is \([-0-9.]\+\),.*/\1/"` + +# mkdir -p does not fail when directories exist already +mkdir -p ../tarballs +cd ../tarballs +TARBALLDIR=`pwd` + +UPSTREAMDIR=${PKG}-${VERSION} + +mkdir -p ${UPSTREAMDIR} +cd ${UPSTREAMDIR} + +tar -xzf ../../TMtools${VERSION}.tar.gz + +rm -rf TMscore TMalign +cd .. + +GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "${UPSTREAMDIR}" +rm -rf "${UPSTREAMDIR}" + Added: trunk/packages/tm-align/trunk/debian/install =================================================================== --- trunk/packages/tm-align/trunk/debian/install (rev 0) +++ trunk/packages/tm-align/trunk/debian/install 2013-08-02 12:34:33 UTC (rev 14317) @@ -0,0 +1,2 @@ +TMalign usr/bin +TMscore usr/bin Added: trunk/packages/tm-align/trunk/debian/manpages =================================================================== --- trunk/packages/tm-align/trunk/debian/manpages (rev 0) +++ trunk/packages/tm-align/trunk/debian/manpages 2013-08-02 12:34:33 UTC (rev 14317) @@ -0,0 +1 @@ +debian/*.1 Added: trunk/packages/tm-align/trunk/debian/rules =================================================================== --- trunk/packages/tm-align/trunk/debian/rules (rev 0) +++ trunk/packages/tm-align/trunk/debian/rules 2013-08-02 12:34:33 UTC (rev 14317) @@ -0,0 +1,28 @@ +#!/usr/bin/make -f +# debian/rules for tm-align + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +PROGNAME=TMalign + +CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) +LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) + +%: + dh $@ + +override_dh_auto_build: + for src in `ls *.f` ; do \ + gfortran -O3 -ffast-math $(CPPFLAGS) $(LDFLAGS) -lm -o `basename $${src} .f` $${src} ; \ + done + +override_dh_auto_clean: + for src in `ls *.f` ; do \ + rm -f `basename $${src} .f` ; \ + done + dh_clean + +get-orig-source: + . debian/get-orig-source + Property changes on: trunk/packages/tm-align/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/tm-align/trunk/debian/source/format =================================================================== --- trunk/packages/tm-align/trunk/debian/source/format (rev 0) +++ trunk/packages/tm-align/trunk/debian/source/format 2013-08-02 12:34:33 UTC (rev 14317) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/tm-align/trunk/debian/upstream =================================================================== --- trunk/packages/tm-align/trunk/debian/upstream (rev 0) +++ trunk/packages/tm-align/trunk/debian/upstream 2013-08-02 12:34:33 UTC (rev 14317) @@ -0,0 +1,16 @@ +Contact: Yang Zhang <[email protected]> +Homepage: http://zhanglab.ccmb.med.umich.edu/TM-align/ +Name: TM-align & TM-score +Reference: + AUTHOR: Y. Zhang, J. Skolnick + TITLE: > + TM-align: A protein structure alignment algorithm based on TM-score + JOURNAL: Nucleic Acids Research + YEAR: 2005 + PAGES: 2302-2309 + VOLUME: 33 + NUMBER: 7 + URL: http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.pdf + ISSN: 1362-4962 + DOI: 10.1093/nar/gki524 + PMID: 15849316 Added: trunk/packages/tm-align/trunk/debian/watch =================================================================== --- trunk/packages/tm-align/trunk/debian/watch (rev 0) +++ trunk/packages/tm-align/trunk/debian/watch 2013-08-02 12:34:33 UTC (rev 14317) @@ -0,0 +1,2 @@ +version=3 +http://zhanglab.ccmb.med.umich.edu/TM-align/TMtools([\d]*)\.tar\.gz _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
