[med-svn] r1799 - trunk/packages/tigr-glimmer/trunk/debian
tille at alioth.debian.org
tille at alioth.debian.org
Tue Apr 22 08:20:37 UTC 2008
Author: tille
Date: 2008-04-22 08:20:36 +0000 (Tue, 22 Apr 2008)
New Revision: 1799
Added:
trunk/packages/tigr-glimmer/trunk/debian/tigr-glimmer
trunk/packages/tigr-glimmer/trunk/debian/tigr-glimmer.1
Removed:
trunk/packages/tigr-glimmer/trunk/debian/glimmer
trunk/packages/tigr-glimmer/trunk/debian/glimmer.1
trunk/packages/tigr-glimmer/trunk/debian/glimmer.substvars
Modified:
trunk/packages/tigr-glimmer/trunk/debian/README.Debian
trunk/packages/tigr-glimmer/trunk/debian/copyright
trunk/packages/tigr-glimmer/trunk/debian/install
trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer3
Log:
renamed glimmer to tigr-glimmer because of name space pollution with gnome,
enhanced docs
Modified: trunk/packages/tigr-glimmer/trunk/debian/README.Debian
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/README.Debian 2008-04-20 07:42:07 UTC (rev 1798)
+++ trunk/packages/tigr-glimmer/trunk/debian/README.Debian 2008-04-22 08:20:36 UTC (rev 1799)
@@ -9,7 +9,8 @@
The upstream authors are very supportive of this debian package for
their software and I thank them for this.
-With version 2.13-1, the binaries and man pages all have a prefix "tigr-"
+In version 2.13-1, the binaries and man pages all have a prefix "tigr-"
to avoid conflicts with other programs, with extract in particular.
+This was changed
- -- Steffen Moeller <moeller at pzr.uni-rostock.de>, Thu, 10 Nov 2004 12:33:46 +0100
+ -- Steffen Moeller <moeller at debian.org>, Thu, 10 Nov 2004 12:33:46 +0100
Modified: trunk/packages/tigr-glimmer/trunk/debian/copyright
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/copyright 2008-04-20 07:42:07 UTC (rev 1798)
+++ trunk/packages/tigr-glimmer/trunk/debian/copyright 2008-04-22 08:20:36 UTC (rev 1799)
@@ -16,7 +16,7 @@
Files: *
Copyright: © 1999-2008
-Copyright: Artistic License
+License: 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.
Deleted: trunk/packages/tigr-glimmer/trunk/debian/glimmer
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/glimmer 2008-04-20 07:42:07 UTC (rev 1798)
+++ trunk/packages/tigr-glimmer/trunk/debian/glimmer 2008-04-22 08:20:36 UTC (rev 1799)
@@ -1,24 +0,0 @@
-#!/bin/sh
-
-BINDIR=/usr/lib/tigr-glimmer
-
-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
Deleted: trunk/packages/tigr-glimmer/trunk/debian/glimmer.1
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/glimmer.1 2008-04-20 07:42:07 UTC (rev 1798)
+++ trunk/packages/tigr-glimmer/trunk/debian/glimmer.1 2008-04-22 08:20:36 UTC (rev 1799)
@@ -1,41 +0,0 @@
-.TH GLIMMER 1 "April 16, 2008"
-.SH NAME
-glimmer \- runs various programs of the TIGR Glimmer suite
-.SH SYNOPSIS
-.B glimmer
-.B program
-[arguments]
-.SH DESCRIPTION
-This manual page documents briefly the
-.B glimmer
-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
-\fBglimmer\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. Please note that the documentation there
-is a part of the former version Glimmer 2. The version Glimmer 3 has
-some features that were described in the notes.pdf document inside
-the documentation directory.
-.PP
-The following programs are included: anomaly, build-fixed, build-icm,
-entropy-profile, entropy-score, extract, glimmer3, long-orfs, multi-extract,
-score-fixed, start-codon-distrib, test, uncovered and window-acgt.
-.SH OPTIONS
-There are no options.
-.SH EXAMPLES
-.IP glimmer\ build-icm
-.IP glimmer\ long-orfs
-.SH SEE ALSO
-For the pre previously packaged version Glimmer2 some text files from
-the documentation were turned to man pages for the Debian GNU/Linux
-distribution by Steffen Moeller <moeller at debian.org>
-.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).
Deleted: trunk/packages/tigr-glimmer/trunk/debian/glimmer.substvars
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/glimmer.substvars 2008-04-20 07:42:07 UTC (rev 1798)
+++ trunk/packages/tigr-glimmer/trunk/debian/glimmer.substvars 2008-04-22 08:20:36 UTC (rev 1799)
@@ -1 +0,0 @@
-shlibs:Depends=libc6 (>= 2.3.2-1), libgcc1 (>= 1:3.3.1-1), libstdc++5 (>= 1:3.3.1-1)
Modified: trunk/packages/tigr-glimmer/trunk/debian/install
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/install 2008-04-20 07:42:07 UTC (rev 1798)
+++ trunk/packages/tigr-glimmer/trunk/debian/install 2008-04-22 08:20:36 UTC (rev 1799)
@@ -1,2 +1,3 @@
-bin/* usr/lib
+bin/* usr/lib/tigr-glimmer
debian/tigr-run-glimmer3 usr/bin
+debian/tigr-glimmer usr/bin
Added: trunk/packages/tigr-glimmer/trunk/debian/tigr-glimmer
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-glimmer (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-glimmer 2008-04-22 08:20:36 UTC (rev 1799)
@@ -0,0 +1,24 @@
+#!/bin/sh
+
+BINDIR=/usr/lib/tigr-glimmer
+
+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-glimmer.1
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-glimmer.1 (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-glimmer.1 2008-04-22 08:20:36 UTC (rev 1799)
@@ -0,0 +1,39 @@
+.TH TIGR-GLIMMER 1 "April 16, 2008"
+.SH NAME
+tigr-glimmer \- runs various programs of the TIGR Glimmer suite
+.SH SYNOPSIS
+.B tigr-glimmer
+.B program
+[arguments]
+.SH DESCRIPTION
+This manual page documents briefly the
+.B tigr-glimmer
+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-glimmer\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. Please note that the documentation there
+is a part of the former version Glimmer 2. The version Glimmer 3 has
+some features that were described in the notes.pdf document inside
+the documentation directory.
+.PP
+The following programs are included: anomaly, build-fixed, build-icm,
+entropy-profile, entropy-score, extract, glimmer3, long-orfs, multi-extract,
+score-fixed, start-codon-distrib, test, uncovered and window-acgt.
+.SH OPTIONS
+There are no options.
+.SH EXAMPLES
+.IP tigr-glimmer\ build-icm
+.IP tigr-glimmer\ long-orfs
+.SH SEE ALSO
+For the pre previously packaged version Glimmer2 some text files from
+the documentation were turned to man pages for the Debian GNU/Linux
+distribution by Steffen Moeller <moeller at debian.org>
+.br
+.SH AUTHORS
+This manual page was written by Andreas Tille <tille at debian.org>, for
+the Debian GNU/Linux system (but may be used by others).
Modified: trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer3
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer3 2008-04-20 07:42:07 UTC (rev 1798)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer3 2008-04-22 08:20:36 UTC (rev 1799)
@@ -3,15 +3,16 @@
clear
echo "Genome is " $1
echo "Find non-overlapping orfs in tmp.coord"
+BINDIR="/usr/lib/tigr-glimmer"
rm -f tmp.coord
-tigr-long-orfs $1 | tigr-get-putative >tmp.coord
-echo "Extract training sequences to tmp.train"
+${BINDIR}/long-orfs $1 | ${BINDIR}/get-putative >tmp.coord
+echo "Extract training sequences to tmp.train"
rm -f tmp.train
-tigr-extract $1 tmp.coord >tmp.train
+${BINDIR}/extract $1 tmp.coord >tmp.train
wc tmp.train
echo "Build interpolated context model in tmp.model"
rm -f tmp.model
-tigr-build-icm <tmp.train >tmp.model
+${BINDIR}/build-icm <tmp.train >tmp.model
echo "Predict genes with Glimmer3 with coordinates in g3.coord"
rm -f g3.coord
-tigr-glimmer3 $1 tmp.model | tigr-get-putative >g3.coord
+${BINDIR}/glimmer3 $1 tmp.model | ${BINDIR}/get-putative >g3.coord
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