diff galaxy-tools/biobank/tools/launcher.sh @ 0:ba6cf6ede027 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/tools/launcher.sh	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,56 @@
+#!/bin/sh                                                                       
+
+CMD=""
+PYTH_PATH="PYTHONPATH=/SHARE/USERFS/els7/users/galaxy/develop/usr-cluster/lib/p\
+ython2.7/site-packages/:/SHARE/USERFS/els7/users/biobank/lib/"
+runner="$(dirname ${BASH_SOURCE[0]})/"
+until [ -z $1 ]
+    do
+
+    opt_host='--host='
+    opt_user='--user='
+    opt_passwd='--passwd='
+    opt_interpreter='--interpreter='
+    opt_runner='--runner='
+    if [[ $1 == $opt_host* ]]; then
+        host=`echo $1 | cut -d '=' -f2 | cut -d '.' -f1`
+        if [ -z $host -o $host == 'None' ]; then
+            echo 'ERROR. Missing omero host parameter. Please, set Omero Host in your user preferences' > /dev/null >&2
+            exit -1
+        fi
+        PYTH_PATH+=$host
+        HOST=`echo $1 | cut -d '=' -f2`
+        CMD+=' '$1
+    elif [[ $1 == $opt_user* ]]; then
+        user=`echo $1 | cut -d '=' -f2`
+        if [ -z $user -o $user == 'None' ]; then
+            echo 'ERROR. Missing omero user parameter. Please, set Omero User in your user preferences' > /dev/null >&2
+            exit -1
+        fi
+        CMD+=' '$1
+    elif [[ $1 == $opt_passwd* ]]; then
+        passwd=`echo $1 | cut -d '=' -f2`
+        if [ -z $passwd -o $passwd == 'None' ]; then
+            echo 'ERROR. Missing omero password parameter. Please, set Omero Password in your user preferences' > /dev/null >&2
+            exit -1
+        fi
+        CMD+=' '$1
+    elif [[ $1 == $opt_runner* ]]; then
+        runner+=`echo $1 | cut -d '=' -f2`
+    elif [[ $1 == $opt_interpreter* ]]; then
+        interpreter=`echo $1 | cut -d '=' -f2`
+    else
+        CMD+=' '$1
+    fi
+    shift
+done
+export $PYTH_PATH/:$PYTHONPATH
+profile="/SHARE/USERFS/els7/users/biobank/lib/${HOST}.biobank.profile"
+if [ -f $profile ]; then
+    source $profile
+    CMD=$interpreter' '$runner$CMD
+    $CMD
+else
+    echo "ERROR. Biobank profile file doesn't exist. Please, check Omero Host in your user preferences" > /dev/null >&2
+    exit -1
+fi