[Swift-commit] r7870 - in SwiftApps/swift-galaxy: . swift swift/old
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Tue May 13 11:29:19 CDT 2014
Author: ketan
Date: 2014-05-13 11:29:19 -0500 (Tue, 13 May 2014)
New Revision: 7870
Added:
SwiftApps/swift-galaxy/setup.py
SwiftApps/swift-galaxy/swift/old/test.sh
Removed:
SwiftApps/swift-galaxy/swift/test.sh
Modified:
SwiftApps/swift-galaxy/swift/testpy.sh
Log:
adding setup for installation
Added: SwiftApps/swift-galaxy/setup.py
===================================================================
--- SwiftApps/swift-galaxy/setup.py (rev 0)
+++ SwiftApps/swift-galaxy/setup.py 2014-05-13 16:29:19 UTC (rev 7870)
@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+
+"""
+Setup script to install swift-galaxy framework to your Galaxy installation.
+"""
+
+import subprocess
+import sys
+import os
+import distutils.spawn
+import traceback
+import fnmatch
+
+galaxyloc=sys.argv[1]
+
+#step 1. Create symlink to the swift directory from the tools directory of galaxyloc if not already present
+os.symlink (os.getcwd()+"/screenshots", galaxyloc+"/tools/screenshots");
+
+#step 2. update the tool_conf.xml
+
+#<section name="swift" id="swift">
+# <tool file="swift/genswift.xml" />
+# <tool file="swift/genericswift.xml" />
+# <tool file="swift/swiftforeach.xml" />
+#</section>
+
+#step 3. Print message
+
+
Property changes on: SwiftApps/swift-galaxy/setup.py
___________________________________________________________________
Added: svn:executable
+ *
Copied: SwiftApps/swift-galaxy/swift/old/test.sh (from rev 7869, SwiftApps/swift-galaxy/swift/test.sh)
===================================================================
--- SwiftApps/swift-galaxy/swift/old/test.sh (rev 0)
+++ SwiftApps/swift-galaxy/swift/old/test.sh 2014-05-13 16:29:19 UTC (rev 7870)
@@ -0,0 +1,41 @@
+#!/bin/bash
+
+#!/bin/bash
+
+cat << EOF > list.txt
+a
+b
+c
+EOF
+
+cat << EOF > x.sh
+#!/bin/bash
+
+echo \$\@
+EOF
+
+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 ""
+
+echo "Range, no input parameters and files"
+./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!"
+
+echo "Range, string input parameters"
+./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 ""
+
+echo "T list"
+./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"
+
+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" "$HOME/swift-sandbox" "/nfs2/ketan/galaxy-dist/database/files/000/dataset_12.dat" "/nfs2/ketan/galaxy-dist/database/files/000/dataset_13.dat" "hello how are you"
Deleted: SwiftApps/swift-galaxy/swift/test.sh
===================================================================
--- SwiftApps/swift-galaxy/swift/test.sh 2014-05-13 14:33:31 UTC (rev 7869)
+++ SwiftApps/swift-galaxy/swift/test.sh 2014-05-13 16:29:19 UTC (rev 7870)
@@ -1,41 +0,0 @@
-#!/bin/bash
-
-#!/bin/bash
-
-cat << EOF > list.txt
-a
-b
-c
-EOF
-
-cat << EOF > x.sh
-#!/bin/bash
-
-echo \$\@
-EOF
-
-chmod 755 x.sh
-
-echo "List, no input parameters and files"
-./swiftforeach.sh list swiftK localhost "" bash x.sh "" list.txt tmpoutlist a.log list1.out ""
-
-echo "Range, no input parameters and files"
-./swiftforeach.sh range swiftK localhost "" bash x.sh "" 0 9 1 tmpoutrange b.log list2.out ""
-
-echo "List, string input parameters"
-./swiftforeach.sh range swiftK localhost "" bash x.sh "" 0 9 1 tmpoutrange b.log list2.out "hello there list!"
-
-echo "Range, string input parameters"
-./swiftforeach.sh range swiftK localhost "" bash x.sh "" 0 9 1 tmpoutrange b.log list2.out "hi there range!"
-
-echo "List, no input parameters and files stdin /dev/null"
-./swiftforeach.sh list swiftK localhost "" bash x.sh "/dev/null" list.txt tmpoutlist a.log list1.out ""
-
-echo "T list"
-./swiftforeach.sh list swiftT localhost "" bash x.sh "" list.txt tmpoutlist a.log list1.out ""
-
-echo "T range"
-./swiftforeach.sh range swiftT localhost "" bash x.sh "" 0 9 1 tmpoutlist a.log list1.out "hello there T"
-
-echo "Call from Galaxy"
-bash /nfs2/ketan/galaxy-dist/tools/swift/swiftforeach.sh "range" "swiftT" "localhost" "" "sh" "/nfs2/ketan/galaxy-dist/database/files/000/dataset_1.dat" "None" "0" "9" "1" "$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"
Modified: SwiftApps/swift-galaxy/swift/testpy.sh
===================================================================
--- SwiftApps/swift-galaxy/swift/testpy.sh 2014-05-13 14:33:31 UTC (rev 7869)
+++ SwiftApps/swift-galaxy/swift/testpy.sh 2014-05-13 16:29:19 UTC (rev 7870)
@@ -37,5 +37,8 @@
echo "T range"
./swiftforeach.py range swiftT localhost "" bash x.sh "" 0 9 1 tmpoutlist a.log list1.out "hello there T"
-echo "Call from Galaxy"
+echo "Call K from Galaxy"
+python /Users/ketan/galaxy-dist/tools/swift/swiftforeach.py "range" "swiftK" "localhost" "swiftarg" "sh" "/Users/ketan/galaxy-dist/database/files/000/dataset_348.dat" "/dev/null" "0" "9" "1" "$HOME/sandbox2" "/Users/ketan/galaxy-dist/database/files/000/dataset_353.dat" "/Users/ketan/galaxy-dist/database/files/000/dataset_354.dat" "hello how are you"
+
+echo "Call T from Galaxy"
python /nfs2/ketan/galaxy-dist/tools/swift/swiftforeach.py "range" "swiftT" "localhost" "" "sh" "/nfs2/ketan/galaxy-dist/database/files/000/dataset_1.dat" "None" "0" "9" "1" "$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"
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