From 61e8df1a2912ba8a477c7b3f3a4e8565b821b7ea Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 20 Oct 2009 13:29:57 +0000
Subject: [PATCH] Added a simple to use wrapper script for "run.pl".
---
misc-scripts/id_mapping/myRun.ksh | 55 +++++++++++++++++++++++++++++++
1 file changed, 55 insertions(+)
create mode 100755 misc-scripts/id_mapping/myRun.ksh
diff --git a/misc-scripts/id_mapping/myRun.ksh b/misc-scripts/id_mapping/myRun.ksh
new file mode 100755
index 0000000000..822ee37994
--- /dev/null
+++ b/misc-scripts/id_mapping/myRun.ksh
@@ -0,0 +1,55 @@
+#!/usr/bin/ksh
+
+scriptname=$0
+
+function usage {
+ cat >&2 <<EOT
+Usage:
+ ${scriptname} -c conf_file [ -m mode ]
+
+ ... where 'conf_file' is the absolute path to the configuration file
+ to use for this stable ID mapping run, and 'mode' is either left out
+ (which is normally the case), or one of
+
+ - check_only
+ - normal (default)
+ - mapping
+ - upload
+
+EOT
+}
+
+if [[ ! -e ./run.pl ]]; then
+ print -u2 "Expected to find the following executable file here:"
+ print -u2 "\trun.pl"
+ exit
+fi
+
+mode="normal"
+
+while getopts 'c:m:' opt; do
+ case ${opt} in
+ c) conf=${OPTARG} ;;
+ m) mode=${OPTARG} ;;
+ *) usage; exit ;;
+ esac
+done
+
+if [[ -z ${conf} || -z ${mode} ]]; then
+ usage
+ exit
+fi
+
+if [[ ! -f ${conf} ]]; then
+ print -u2 "The file '${conf}' does not exist."
+ exit
+fi
+
+if [[ ${conf#/} == ${conf} ]]; then
+ print -u2 "The path '${conf}' is not absolute."
+ exit
+fi
+
+./run.pl --lsf --conf=${conf} --logauto --mode=${mode}
+
+# $Id$
--
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