[med-svn] r1800 - in trunk/packages/tigr-glimmer/trunk/debian: . bin
tille at alioth.debian.org
tille at alioth.debian.org
Tue Apr 22 09:48:42 UTC 2008
Author: tille
Date: 2008-04-22 09:48:41 +0000 (Tue, 22 Apr 2008)
New Revision: 1800
Added:
trunk/packages/tigr-glimmer/trunk/debian/bin/
trunk/packages/tigr-glimmer/trunk/debian/bin/tigr-glimmer
trunk/packages/tigr-glimmer/trunk/debian/bin/tigr-run-glimmer3
Removed:
trunk/packages/tigr-glimmer/trunk/debian/index.html
trunk/packages/tigr-glimmer/trunk/debian/tigr-glimmer
trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer3
Modified:
trunk/packages/tigr-glimmer/trunk/debian/README.Debian
trunk/packages/tigr-glimmer/trunk/debian/install
Log:
Moved scripts to debian/bin to avoid name conflict with package target dir, removed redundant index.html which is a copy of tigr-extract(1); enhanced README.Debian
Modified: trunk/packages/tigr-glimmer/trunk/debian/README.Debian
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/README.Debian 2008-04-22 08:20:36 UTC (rev 1799)
+++ trunk/packages/tigr-glimmer/trunk/debian/README.Debian 2008-04-22 09:48:41 UTC (rev 1800)
@@ -11,6 +11,13 @@
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
+This was changed in the current packaging of version 3.x in favour of
+putting the executables under /usr/lib/tigr-glimmer. A wrapper is
+provided that enables to call the binaries via
+ tigr-glimmer <binary>
+
+(see man tigr-glimmer). Alternatively you might add this directory
+to your search PATH to call the binaries directly.
+
-- Steffen Moeller <moeller at debian.org>, Thu, 10 Nov 2004 12:33:46 +0100
Added: trunk/packages/tigr-glimmer/trunk/debian/bin/tigr-glimmer
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/bin/tigr-glimmer (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/bin/tigr-glimmer 2008-04-22 09:48:41 UTC (rev 1800)
@@ -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/bin/tigr-run-glimmer3
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/bin/tigr-run-glimmer3 (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/bin/tigr-run-glimmer3 2008-04-22 09:48:41 UTC (rev 1800)
@@ -0,0 +1,18 @@
+#!/bin/sh
+echo "run Glimmer3"
+clear
+echo "Genome is " $1
+echo "Find non-overlapping orfs in tmp.coord"
+BINDIR="/usr/lib/tigr-glimmer"
+rm -f tmp.coord
+${BINDIR}/long-orfs $1 | ${BINDIR}/get-putative >tmp.coord
+echo "Extract training sequences to tmp.train"
+rm -f tmp.train
+${BINDIR}/extract $1 tmp.coord >tmp.train
+wc tmp.train
+echo "Build interpolated context model in tmp.model"
+rm -f tmp.model
+${BINDIR}/build-icm <tmp.train >tmp.model
+echo "Predict genes with Glimmer3 with coordinates in g3.coord"
+rm -f g3.coord
+${BINDIR}/glimmer3 $1 tmp.model | ${BINDIR}/get-putative >g3.coord
Property changes on: trunk/packages/tigr-glimmer/trunk/debian/bin/tigr-run-glimmer3
___________________________________________________________________
Name: svn:executable
+ *
Deleted: trunk/packages/tigr-glimmer/trunk/debian/index.html
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/index.html 2008-04-22 08:20:36 UTC (rev 1799)
+++ trunk/packages/tigr-glimmer/trunk/debian/index.html 2008-04-22 09:48:41 UTC (rev 1800)
@@ -1,168 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<HTML
-><HEAD
-><TITLE
->EXTRACT</TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"></HEAD
-><BODY
-CLASS="REFENTRY"
-BGCOLOR="#FFFFFF"
-TEXT="#000000"
-LINK="#0000FF"
-VLINK="#840084"
-ALINK="#0000FF"
-><H1
-><A
-NAME="AEN1"
-></A
->EXTRACT</H1
-><DIV
-CLASS="REFNAMEDIV"
-><A
-NAME="AEN15"
-></A
-><H2
->Name</H2
->extract -- Fine start/stop positions of genes in genome sequence</DIV
-><DIV
-CLASS="REFSYNOPSISDIV"
-><A
-NAME="AEN18"
-></A
-><H2
->Synopsis</H2
-><P
-><B
-CLASS="COMMAND"
->long-orgs</B
-> [genome-file <VAR
-CLASS="OPTION"
-><VAR
-CLASS="REPLACEABLE"
->options</VAR
-></VAR
->]</P
-></DIV
-><DIV
-CLASS="REFSECT1"
-><A
-NAME="AEN24"
-></A
-><H2
->DESCRIPTION</H2
-><P
->Program extract takes a FASTA format sequence file and a file
-with a list of start/stop positions in that file (e.g., as produced
-by the long-orfs program) and extracts and outputs the
-specified sequences.</P
-><P
->The first command-line argument is the name of the sequence file,
-which must be in FASTA format.</P
-><P
->The second command-line argument is the name of the coordinate file.
-It must contain a list of pairs of positions in the first file, one
-per line. The format of each entry is:</P
-><P
-> <IDstring>> <start position> <stop position></P
-><P
->This file should contain no other information, so if you're using
-the output of glimmer or long-orfs , you'll have to cut off
-header lines.</P
-><P
->The output of the program goes to the standard output and has one
-line for each line in the coordinate file. Each line contains
-the IDstring , followed by white space, followed by the substring
-of the sequence file specified by the coordinate pair. Specifically,
-the substring starts at the first position of the pair and ends at
-the second position (inclusive). If the first position is bigger
-than the second, then the DNA reverse complement of each position
-is generated. Start/stop pairs that "wrap around" the end of the
-genome are allowed.</P
-></DIV
-><DIV
-CLASS="REFSECT1"
-><A
-NAME="AEN32"
-></A
-><H2
->OPTIONS</H2
-><P
-></P
-><DIV
-CLASS="VARIABLELIST"
-><DL
-><DT
-><VAR
-CLASS="OPTION"
->-skip</VAR
-></DT
-><DD
-><P
-> makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the behaviour of the previous version of the program.</P
-></DD
-><DT
-><VAR
-CLASS="OPTION"
->-l</VAR
-></DT
-><DD
-><P
-> makes the output omit an sequences shorter than n characters.
- n includes the 3 skipped characters if the -skip switch
- is one.
- </P
-></DD
-></DL
-></DIV
-></DIV
-><DIV
-CLASS="REFSECT1"
-><A
-NAME="AEN45"
-></A
-><H2
->SEE ALSO</H2
-><P
->glimmer2 (1),
-long-orfs (1),
-adjust (1),
-anomaly (1),
-build-icm (1),
-check (1),
-codon-usage (1),
-compare-lists (1),
-extract (1),
-generate (1),
-get-len (1),
-get-putative (1),</P
-><P
->http://www.tigr.org/software/glimmer/</P
-><P
->Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</P
-></DIV
-><DIV
-CLASS="REFSECT1"
-><A
-NAME="AEN50"
-></A
-><H2
->AUTHOR</H2
-><P
->This manual page was quickly copied from the glimmer web site by Steffen Moeller <CODE
-CLASS="EMAIL"
-><<A
-HREF="mailto:moeller at pzr.uni-rostock.de"
->moeller at pzr.uni-rostock.de</A
->></CODE
-> for
- the <SPAN
-CLASS="PRODUCTNAME"
->Debian</SPAN
-> system.
- </P
-></DIV
-></BODY
-></HTML
->
\ No newline at end of file
Modified: trunk/packages/tigr-glimmer/trunk/debian/install
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/install 2008-04-22 08:20:36 UTC (rev 1799)
+++ trunk/packages/tigr-glimmer/trunk/debian/install 2008-04-22 09:48:41 UTC (rev 1800)
@@ -1,3 +1,2 @@
bin/* usr/lib/tigr-glimmer
-debian/tigr-run-glimmer3 usr/bin
-debian/tigr-glimmer usr/bin
+debian/bin/* usr/bin
Deleted: trunk/packages/tigr-glimmer/trunk/debian/tigr-glimmer
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-glimmer 2008-04-22 08:20:36 UTC (rev 1799)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-glimmer 2008-04-22 09:48:41 UTC (rev 1800)
@@ -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/tigr-run-glimmer3
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer3 2008-04-22 08:20:36 UTC (rev 1799)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-run-glimmer3 2008-04-22 09:48:41 UTC (rev 1800)
@@ -1,18 +0,0 @@
-#!/bin/sh
-echo "run Glimmer3"
-clear
-echo "Genome is " $1
-echo "Find non-overlapping orfs in tmp.coord"
-BINDIR="/usr/lib/tigr-glimmer"
-rm -f tmp.coord
-${BINDIR}/long-orfs $1 | ${BINDIR}/get-putative >tmp.coord
-echo "Extract training sequences to tmp.train"
-rm -f tmp.train
-${BINDIR}/extract $1 tmp.coord >tmp.train
-wc tmp.train
-echo "Build interpolated context model in tmp.model"
-rm -f tmp.model
-${BINDIR}/build-icm <tmp.train >tmp.model
-echo "Predict genes with Glimmer3 with coordinates in g3.coord"
-rm -f g3.coord
-${BINDIR}/glimmer3 $1 tmp.model | ${BINDIR}/get-putative >g3.coord
More information about the debian-med-commit
mailing list