[Swift-commit] r7835 - SwiftApps/swift-galaxy/swift

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2014-05-08 16:31:09 -0500 (Thu, 08 May 2014)
New Revision: 7835

Modified:
   SwiftApps/swift-galaxy/swift/swiftforeach.sh
   SwiftApps/swift-galaxy/swift/swiftforeach.xml
   SwiftApps/swift-galaxy/swift/test.sh
Log:
test for T

Modified: SwiftApps/swift-galaxy/swift/swiftforeach.sh
===================================================================
--- SwiftApps/swift-galaxy/swift/swiftforeach.sh	2014-05-07 15:18:01 UTC (rev 7834)
+++ SwiftApps/swift-galaxy/swift/swiftforeach.sh	2014-05-08 21:31:09 UTC (rev 7835)
@@ -1,7 +1,7 @@
 #!/bin/bash
-
 # originally list
 
+#echo $@ > /tmp/args.txt
 #set workdir
 wdir=$(mktemp -d /tmp/swift-gal.XXXX)
 
@@ -234,24 +234,31 @@
 
 EXITCODE=0
 case $sites in  
-  "Localhost" )
+  "localhost" )
+   echo "in localhost" >> /tmp/status.txt
    STC=$(\which stc)
+   echo "got stc" >> /tmp/status.txt
    turbine=$(\which turbine)
+   echo "got turbine" >> /tmp/status.txt
    $STC -j $(\which java) $wdir/script.swift 2>$logfile
+   echo "done running stc" >> /tmp/status.txt
+   echo $turbine -n $n $wdir/script.tcl "${swiftargs}" >> /tmp/status.txt
    $turbine -n $n $wdir/script.tcl "${swiftargs}"
+   echo "done running turbine, for $n" >> /tmp/status.txt
    EXITCODE=$?
+   echo "exit code obtained" >> /tmp/status.txt
 	;;
 "Vesta" )
   TURBINE_HOME=/home/wozniak/Public/sfw/turbine
   STC=/home/wozniak/Public/sfw/stc/bin/stc
-  $STC -j $(\which java) -t checkpointing -r ${PWD} $wdir/script.swift "${swiftargs}" 2>$logfile
+  $STC -j $(\which java) -t checkpointing -r ${PWD} $wdir/script.swift 2>$logfile
   $TURBINE_HOME/scripts/submit/cobalt/turbine-cobalt-run.zsh -n $n -s $HOME/cf $wdir/script.tcl
   EXITCODE=$?
 	;;
 "Mira" )
   TURBINE_HOME=/home/wozniak/Public/sfw/ppc64/turbine
   STC=/home/wozniak/Public/sfw/ppc64/stc/bin/stc
-  $STC -j $(\which java) -t checkpointing -r ${PWD} $wdir/script.swift "${swiftargs}" 2>$logfile
+  $STC -j $(\which java) -t checkpointing -r ${PWD} $wdir/script.swift 2>$logfile
   $TURBINE_HOME/scripts/submit/cobalt/turbine-cobalt-run.zsh -n $n -i $HOME/prerun.sh -s $HOME/cf $wdir/script.tcl
   EXITCODE=$?
 	;;
@@ -266,5 +273,6 @@
 if [ "$EXITCODE" -ne "0" ]; then
       cat $logfile >&2
 fi
+
 exit $EXITCODE
 

Modified: SwiftApps/swift-galaxy/swift/swiftforeach.xml
===================================================================
--- SwiftApps/swift-galaxy/swift/swiftforeach.xml	2014-05-07 15:18:01 UTC (rev 7834)
+++ SwiftApps/swift-galaxy/swift/swiftforeach.xml	2014-05-08 21:31:09 UTC (rev 7835)
@@ -158,7 +158,7 @@
 
         <param name="swiftargs" size="60" type="text" label="swiftargs" help="Add Swift level commandline arguments" />
 
-        <param name="outloc" size="50" type="text" value="$HOME/swift-sandbox" label="location for output files" help="Swift will write output files here on disc">
+        <param name="outloc" size="50" type="text" value="$HOME/sandbox" label="location for output files" help="Swift will write output files here on disc">
             <sanitizer sanitize="False" />
         </param>
     </inputs>

Modified: SwiftApps/swift-galaxy/swift/test.sh
===================================================================
--- SwiftApps/swift-galaxy/swift/test.sh	2014-05-07 15:18:01 UTC (rev 7834)
+++ SwiftApps/swift-galaxy/swift/test.sh	2014-05-08 21:31:09 UTC (rev 7835)
@@ -17,22 +17,25 @@
 chmod 755 x.sh
 
 echo "List, no input parameters and files"
-./swiftforeach.sh list swiftK Localhost "" bash x.sh "" list.txt tmpoutlist a.log list1.out ""
+./swiftforeach.sh list swiftK localhost "" bash x.sh "" list.txt tmpoutlist a.log list1.out ""
 
 echo "Range, no input parameters and files"
-./swiftforeach.sh range swiftK Localhost "" bash x.sh "" 0 9 1 tmpoutrange b.log list2.out ""
+./swiftforeach.sh range swiftK localhost "" bash x.sh "" 0 9 1 tmpoutrange b.log list2.out ""
 
 echo "List, string input parameters"
-./swiftforeach.sh range swiftK Localhost "" bash x.sh "" 0 9 1 tmpoutrange b.log list2.out "hello there list!"
+./swiftforeach.sh range swiftK localhost "" bash x.sh "" 0 9 1 tmpoutrange b.log list2.out "hello there list!"
 
 echo "Range, string input parameters"
-./swiftforeach.sh range swiftK Localhost "" bash x.sh "" 0 9 1 tmpoutrange b.log list2.out "hi there range!"
+./swiftforeach.sh range swiftK localhost "" bash x.sh "" 0 9 1 tmpoutrange b.log list2.out "hi there range!"
 
 echo "List, no input parameters and files stdin /dev/null"
-./swiftforeach.sh list swiftK Localhost "" bash x.sh "/dev/null" list.txt tmpoutlist a.log list1.out ""
+./swiftforeach.sh list swiftK localhost "" bash x.sh "/dev/null" list.txt tmpoutlist a.log list1.out ""
 
 echo "T list"
-./swiftforeach.sh list swiftT Localhost "" bash x.sh "" list.txt tmpoutlist a.log list1.out ""
+./swiftforeach.sh list swiftT localhost "" bash x.sh "" list.txt tmpoutlist a.log list1.out ""
 
 echo "T range"
-./swiftforeach.sh range swiftT Localhost "" bash x.sh "" 0 9 1 tmpoutlist a.log list1.out "hello there T"
+./swiftforeach.sh range swiftT localhost "" bash x.sh "" 0 9 1 tmpoutlist a.log list1.out "hello there T"
+
+echo "Call from Galaxy"
+bash /nfs2/ketan/galaxy-dist/tools/swift/swiftforeach.sh "range" "swiftT" "localhost" "" "sh" "/nfs2/ketan/galaxy-dist/database/files/000/dataset_1.dat" "None" "0" "9" "1" "$HOME/swift-sandbox" "/nfs2/ketan/galaxy-dist/database/files/000/dataset_12.dat" "/nfs2/ketan/galaxy-dist/database/files/000/dataset_13.dat" "hello how are you"