[med-svn] r14317 - in trunk/packages/tm-align: . trunk trunk/debian trunk/debian/source
Andreas Tille
tille at alioth.debian.org
Fri Aug 2 12:34:34 UTC 2013
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 <tille at debian.org> 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 <moeller at debian.org>,
+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. No user-serviceable parts.
+. \" fudge factors for nroff and troff
+.if n \{\
+. ds #H 0
+. ds #V .8m
+. ds #F .3m
+. ds #[ \f1
+. ds #] \fP
+.\}
+.if t \{\
+. ds #H ((1u-(\\\\n(.fu%2u))*.13m)
+. ds #V .6m
+. ds #F 0
+. ds #[ \&
+. ds #] \&
+.\}
+. \" simple accents for nroff and troff
+.if n \{\
+. ds ' \&
+. ds ` \&
+. ds ^ \&
+. ds , \&
+. ds ~ ~
+. ds /
+.\}
+.if t \{\
+. ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
+. ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
+. ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
+. ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
+. ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
+. ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
+.\}
+. \" troff and (daisy-wheel) nroff accents
+.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
+.ds 8 \h'\*(#H'\(*b\h'-\*(#H'
+.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
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+.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
+.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
+.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
+.ds ae a\h'-(\w'a'u*4/10)'e
+.ds Ae A\h'-(\w'A'u*4/10)'E
+. \" corrections for vroff
+.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
+.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
+. \" for low resolution devices (crt and lpr)
+.if \n(.H>23 .if \n(.V>19 \
+\{\
+. ds : e
+. ds 8 ss
+. ds o a
+. ds d- d\h'-1'\(ga
+. ds D- D\h'-1'\(hy
+. ds th \o'bp'
+. ds Th \o'LP'
+. ds ae ae
+. ds Ae AE
+.\}
+.rm #[ #] #H #V #F C
+.\" ========================================================================
+.\"
+.IX Title "TMSCORE 1"
+.TH TMSCORE 1 "2011-02-03" .\" "perl v5.10.1" "User Contributed Perl Documentation"
+.\" For nroff, turn off justification. 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: zhng at umich.edu.
+.PP
+This manpage was compiled by Tim Booth (tbooth at ceh.ac.uk)
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: zhng at umich.edu.
+
+This manpage was compiled by Tim Booth (tbooth at ceh.ac.uk)
+
+=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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <moeller at debian.org> Sat, 05 Feb 2011 12:43:32 +0100
+
+tm-align (20110130-1) UNRELEASED; urgency=low
+
+ * Initial release.
+
+ -- Andreas Tille <tille at debian.org> 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 <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) UNRELEASED; urgency=low
+
+ * Initial packaging.
+
+ -- Steffen Moeller <moeller at debian.org> 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 <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>,
+ Andreas Tille <tille at debian.org>
+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 <zhng at umich.edu>
+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 <tbooth at ceh.ac.uk>,
+ © 2011-2012 Andreas Tille <tille at debian.org>
+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 <zhng at umich.edu>
+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
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