[med-svn] r1797 - trunk/packages/tigr-glimmer/trunk/debian
tille at alioth.debian.org
tille at alioth.debian.org
Sat Apr 19 20:40:02 UTC 2008
Author: tille
Date: 2008-04-19 20:40:00 +0000 (Sat, 19 Apr 2008)
New Revision: 1797
Added:
trunk/packages/tigr-glimmer/trunk/debian/tigr
trunk/packages/tigr-glimmer/trunk/debian/tigr.1
Modified:
trunk/packages/tigr-glimmer/trunk/debian/control
trunk/packages/tigr-glimmer/trunk/debian/copyright
Log:
Fixed Homepage, Download; machine readable copyright; wrapper script + manpage
Modified: trunk/packages/tigr-glimmer/trunk/debian/control
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/control 2008-04-18 18:42:23 UTC (rev 1796)
+++ trunk/packages/tigr-glimmer/trunk/debian/control 2008-04-19 20:40:00 UTC (rev 1797)
@@ -7,7 +7,7 @@
Andreas Tille <tille at debian.org>
Build-Depends: debhelper (>= 5.0), docbook-to-man, cdbs, quilt
Standards-Version: 3.7.3
-Homepage: http://www.tigr.org/software/glimmer/
+Homepage: http://www.cbcb.umd.edu/software/glimmer
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/tigr-glimmer/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/tigr-glimmer/trunk/
Modified: trunk/packages/tigr-glimmer/trunk/debian/copyright
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/copyright 2008-04-18 18:42:23 UTC (rev 1796)
+++ trunk/packages/tigr-glimmer/trunk/debian/copyright 2008-04-19 20:40:00 UTC (rev 1797)
@@ -1,137 +1,24 @@
-This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
-Thu, 16 Oct 2003 17:33:46 +0200.
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>
+X-Debianized-Date: Thu, 16 Oct 2003 17:33:46 +0200.
+X-Source-Downloaded-From: http://www.cbcb.umd.edu/software/glimmer
+X-Upstream-Author: Art Delcher <adelcher at tigr.org>,
+ Steven Salzberg <salzberg at tigr.org>
-It was downloaded from ftp://ftp.tigr.org/software/glimmer/
+Files: debian/*
+Copyright: © 2003—2008 Steffen Moeller <moeller at debian.org>
+ © 2003—2008 Andreas Tille <tille at debian.org>
+ © 2008 Charles Plessy <charles-debian-nospam at plessy.org>
+License: GPL-2+
+X-Comment: On Debian systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL'.
-Upstream Authors:
- Art Delcher <adelcher at tigr.org>
- Steven Salzberg <salzberg at tigr.org>
-
-Copyright:
-
--=- Glimmer 2.1x COPYRIGHT NOTICE -=-
-
-Copyright (c) 1998-2003 by The Institute for Genomic
-Research (TIGR), Rockville, Maryland, U.S.A. All rights reserved.
-
-This software is OSI Certified Open Source Software. OSI Certified is a
-certification mark of the Open Source Initiative. Please refer to the
-'LICENSE' file for more information and the 'ACKNOWLEDGEMENTS' file for
-names of contributors to the code base.
-
--=- GLIMMER 2.1x OPEN SOURCE LICENSE -=-
-
-The Artistic License
-
-Preamble
-
-The intent of this document is to state the conditions under which a
-Package may be copied, such that the Copyright Holder maintains some
-semblance of artistic control over the development of the package,
-while giving the users of the package the right to use and distribute
-the Package in a more-or-less customary fashion, plus the right to
-make reasonable modifications.
-
-Definitions:
- * "Package" refers to the collection of files distributed by the
- Copyright Holder, and derivatives of that collection of files
- created through textual modification.
- * "Standard Version" refers to such a Package if it has not been
- modified, or has been modified in accordance with the wishes of
- the Copyright Holder.
- * "Copyright Holder" is whoever is named in the copyright or
- copyrights for the package.
- * "You" is you, if you're thinking about copying or distributing
- this Package.
- * "Reasonable copying fee" is whatever you can justify on the
- basis of media cost, duplication charges, time of people
- involved, and so on. (You will not be required to justify it to
- the Copyright Holder, but only to the computing community at
- large as a market that must bear the fee.)
- * "Freely Available" means that no fee is charged for the item
- itself, though there may be fees involved in handling the
- item. It also means that recipients of the item may redistribute
- it under the same conditions they received it.
-
-1. You may make and give away verbatim copies of the source form of
- the Standard Version of this Package without restriction, provided
- that you duplicate all of the original copyright notices and
- associated disclaimers.
-
-2. You may apply bug fixes, portability fixes and other modifications
- derived from the Public Domain or from the Copyright Holder. A
- Package modified in such a way shall still be considered the
- Standard Version.
-
-3. You may otherwise modify your copy of this Package in any way,
- provided that you insert a prominent notice in each changed file
- stating how and when you changed that file, and provided that you
- do at least ONE of the following:
-
- a) place your modifications in the Public Domain or otherwise make
- them Freely Available, such as by posting said modifications to
- Usenet or an equivalent medium, or placing the modifications on a
- major archive site such as ftp.uu.net, or by allowing the
- Copyright Holder to include your modifications in the Standard
- Version of the Package.
-
- b) use the modified Package only within your corporation or
- organization.
-
- c) rename any non-standard executables so the names do not
- conflict with standard executables, which must also be provided,
- and provide a separate manual page for each non-standard
- executable that clearly documents how it differs from the Standard
- Version.
-
- d) make other distribution arrangements with the Copyright Holder.
-
-4. You may distribute the programs of this Package in object code or
- executable form, provided that you do at least ONE of the
- following:
-
- a) distribute a Standard Version of the executables and library
- files, together with instructions (in the manual page or
- equivalent) on where to get the Standard Version.
-
- b) accompany the distribution with the machine-readable source of
- the Package with your modifications.
-
- c) accompany any non-standard executables with their corresponding
- Standard Version executables, giving the non-standard executables
- non-standard names, and clearly documenting the differences in
- manual pages (or equivalent), together with instructions on where
- to get the Standard Version.
-
- d) make other distribution arrangements with the Copyright Holder.
-
-5. You may charge a reasonable copying fee for any distribution of
- this Package. You may charge any fee you choose for support of this
- Package. You may not charge a fee for this Package itself. However,
- you may distribute this Package in aggregate with other (possibly
- commercial) programs as part of a larger (possibly commercial)
- software distribution provided that you do not advertise this
- Package as a product of your own.
-
-6. The scripts and library files supplied as input to or produced as
- output from the programs of this Package do not automatically fall
- under the copyright of this Package, but belong to whomever
- generated them, and may be sold commercially, and may be aggregated
- with this Package.
-
-7. C or perl subroutines supplied by you and linked into this Package
- shall not be considered part of this Package.
-
-8. The name of the Copyright Holder may not be used to endorse or
- promote products derived from this software without specific prior
- written permission.
-
-9. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
- WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
- OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-
-The End
-This license is approved by the Open Source Initiative
-(www.opensource.org) for certifying software as OSI Certified Open
-Source.
-
+Files: *
+Copyright: © 1999-2008
+Copyright: Artistic License
+ THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
+ IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
+ WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ On Debian systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/Artistic'.
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr 2008-04-19 20:40:00 UTC (rev 1797)
@@ -0,0 +1,24 @@
+#!/bin/sh
+
+BINDIR=/usr/lib/tigr
+
+if [ $# -lt 1 ] ; then
+ echo "Usage: $0 <program>" 1>&2
+ echo " Existing programs are:"
+ ls ${BINDIR}
+ exit 1
+fi
+
+WRAPPER=$0
+PROGRAM=$1
+shift
+ARGS=$*
+
+if [ -x ${BINDIR}/${PROGRAM} ]; then
+ exec ${BINDIR}/${PROGRAM} ${ARGS}
+else
+ echo "Usage: ${PROGRAM} does not exist in Tigr Glimmer"
+ echo " Existing programs are:"
+ ls ${BINDIR}
+ exit 1
+fi
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr.1
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr.1 (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr.1 2008-04-19 20:40:00 UTC (rev 1797)
@@ -0,0 +1,37 @@
+.TH TIGR 1 "April 16, 2008"
+.SH NAME
+tigr \- runs various programs of the TIGR Glimmer suite
+.SH SYNOPSIS
+.B tigr
+.B program
+[arguments]
+.SH DESCRIPTION
+This manual page documents briefly the
+.B tigr
+wrapper to the TIGR Glimmer programs.
+This manual page was written for the Debian GNU/Linux distribution
+because upstream does not provide this wrapper and it was invented
+for Debian to avoid conflicts with other packages that might cause
+a name space polution.
+.PP
+\fBtigr\fP is just a wrapper that invokes the various programs in the
+TIGR Glimmer software package. You can get more detailed documentation
+in /usr/share/doc/tigr-glimmer where
+you find one helpfile for each program.
+.PP
+The following programs are included: clique, contrast, dnainvar, dnamove, dollop,
+drawgram, fitch, mix, penny, restml, consense, dnacomp, dnaml, dnapars, dolmove, drawtree,
+gendist, move, protdist, retree, contml, dnadist, dnamlk, dnapenny, dolpenny, factor,
+kitsch, neighbor, protpars, and seqboot.
+.SH OPTIONS
+There are no options.
+.SH EXAMPLES
+.IP phylip\ dnapenny
+.IP phylip\ factor
+.SH SEE ALSO
+.BR treetool (1),
+.br
+.SH AUTHOR
+This manual page was written by Stephane Bortzmeyer <bortzmeyer at debian.org>
+and Dr. Guenter Bechly <gbechly at debian.org>, for the Debian GNU/Linux system
+(but may be used by others).
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