[med-svn] r731 - in trunk/packages/tm-align/trunk: . debian
smoe-guest at alioth.debian.org
smoe-guest at alioth.debian.org
Sun Oct 21 19:04:55 UTC 2007
Author: smoe-guest
Date: 2007-10-21 19:04:55 +0000 (Sun, 21 Oct 2007)
New Revision: 731
Added:
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/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/dirs
trunk/packages/tm-align/trunk/debian/rules
Log:
[svn-inject] Applying Debian modifications to trunk
Property changes on: trunk/packages/tm-align/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
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 2007-10-21 19:04:55 UTC (rev 731)
@@ -0,0 +1,19 @@
+tm-align for Debian
+-------------------
+
+This program was not yet tested, it is only provided as a first
+hunch of what is there and what needs to be done.
+
+Remaining work:
+
+ * man page
+ * testing with examples
+ * some meta-instructions on what similar software is out there in Debian
+ to be used with TM-align.
+ * spelling should be made consistent between public appearance on
+ web pages (TM-align), the executable (TMalign), and the Debian
+ package tm-align.
+ * Copyright information is still unclear.
+ * The program has not yet been tested.
+
+ -- Steffen Moeller <moeller at debian.org> Sun, 21 Oct 2007 17:11:53 +0200
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 2007-10-21 19:04:55 UTC (rev 731)
@@ -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/changelog
===================================================================
--- trunk/packages/tm-align/trunk/debian/changelog (rev 0)
+++ trunk/packages/tm-align/trunk/debian/changelog 2007-10-21 19:04:55 UTC (rev 731)
@@ -0,0 +1,6 @@
+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
+
Added: trunk/packages/tm-align/trunk/debian/compat
===================================================================
--- trunk/packages/tm-align/trunk/debian/compat (rev 0)
+++ trunk/packages/tm-align/trunk/debian/compat 2007-10-21 19:04:55 UTC (rev 731)
@@ -0,0 +1 @@
+5
Added: trunk/packages/tm-align/trunk/debian/control
===================================================================
--- trunk/packages/tm-align/trunk/debian/control (rev 0)
+++ trunk/packages/tm-align/trunk/debian/control 2007-10-21 19:04:55 UTC (rev 731)
@@ -0,0 +1,18 @@
+Source: tm-align
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 5), gfortran
+Standards-Version: 3.7.2
+Homepage: http://zhang.bioinformatics.ku.edu/TM-align/
+
+Package: tm-align
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: pymol, rasmol
+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 2007-10-21 19:04:55 UTC (rev 731)
@@ -0,0 +1,26 @@
+This package was debianized by Steffen Moeller <moeller at debian.org> on
+Sun, 21 Oct 2007 17:11:53 +0200.
+
+It was downloaded from http://zhang.bioinformatics.ku.edu/TM-align/
+
+Upstream Authors:
+
+ Yang Zhang <yzhang at ku.edu>
+ Jeffrey Skolnick
+
+
+right:
+
+ Yang Zhang <yzhang at ku.edu>
+ Jeffrey Skolnick
+
+ The copyrights of the employing universities is still unclear,
+ upstream still needs to be contacted.
+
+License:
+
+ The program can be freely copied or modified or redistributed.
+
+The Debian packaging is (C) 2007, Steffen Moeller <moeller at debian.org> and
+is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
+
Added: trunk/packages/tm-align/trunk/debian/dirs
===================================================================
--- trunk/packages/tm-align/trunk/debian/dirs (rev 0)
+++ trunk/packages/tm-align/trunk/debian/dirs 2007-10-21 19:04:55 UTC (rev 731)
@@ -0,0 +1 @@
+usr/bin
Added: trunk/packages/tm-align/trunk/debian/rules
===================================================================
--- trunk/packages/tm-align/trunk/debian/rules (rev 0)
+++ trunk/packages/tm-align/trunk/debian/rules 2007-10-21 19:04:55 UTC (rev 731)
@@ -0,0 +1,76 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+
+PROGNAME=TMalign
+
+configure: configure-stamp
+configure-stamp:
+ dh_testdir
+ # Add here commands to configure the package.
+
+ touch configure-stamp
+
+
+build: build-stamp
+
+build-stamp: configure-stamp
+ dh_testdir
+ gfortran -o $(PROGNAME) TMalign.f
+ touch $@
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp
+ dh_clean $(PROGNAME)
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+
+binary-indep: build install
+# We have nothing to do by default.
+
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_install $(PROGNAME) usr/bin
+ dh_installman debian/$(PROGNAME).1
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-arch
+
+get-orig-source:
+ mkdir tm-align-tmp
+ ( cd tm-align-tmp && wget http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f ) ; \
+ version=`grep -A1 history tm-align-tmp/TMalign.f | tail -1 | cut -f1 -d: | tr -d ' */'` ; \
+ 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
+
+.PHONY: build clean binary-indep binary-arch binary install configure
Property changes on: trunk/packages/tm-align/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
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