[Swift-commit] r8369 - SwiftApps/ematter/galaxy
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Wed Jan 21 12:43:42 CST 2015
Author: ketan
Date: 2015-01-21 12:43:42 -0600 (Wed, 21 Jan 2015)
New Revision: 8369
Added:
SwiftApps/ematter/galaxy/smeagol0.swift
SwiftApps/ematter/galaxy/swiftsmeagol0.py
Modified:
SwiftApps/ematter/galaxy/smeagol0.xml
Log:
smeagol0
Added: SwiftApps/ematter/galaxy/smeagol0.swift
===================================================================
--- SwiftApps/ematter/galaxy/smeagol0.swift (rev 0)
+++ SwiftApps/ematter/galaxy/smeagol0.swift 2015-01-21 18:43:42 UTC (rev 8369)
@@ -0,0 +1,34 @@
+type file;
+
+
+app (file _tio2auhm, file _tio2audm,
+ file _out) smeagol0_app ( file _au3dm, file _au3hst, file _aupsf,
+ file _ausicpsf, file _bulklft, file _bulkrgt,
+ file _inputfdf, file _opsf, file _osicpsf,
+ file _tipsf, file _tisicpsf )
+{
+ mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out;
+}
+
+file au3dm <single_file_mapper; file=arg("au3dm")>;
+file au3hst <single_file_mapper; file=arg("au3hst")>;
+file aupsf <single_file_mapper; file=arg("aupsf")>;
+file ausicpsf <single_file_mapper; file=arg("ausicpsf")>;
+file bulklft <single_file_mapper; file=arg("bulklft")>;
+file bulkrgt <single_file_mapper; file=arg("bulkrgt")>;
+file inputfdf <single_file_mapper; file=arg("inputfdf")>;
+file opsf <single_file_mapper; file=arg("opsf")>;
+file osicpsf <single_file_mapper; file=arg("osicpsf")>;
+file tipsf <single_file_mapper; file=arg("tipsf")>;
+file tisicpsf <single_file_mapper; file=arg("tisicpsf")>;
+
+file tio2auhm <single_file_mapper; file=arg("tio2auhm")>;
+file tio2audm <single_file_mapper; file=arg("tio2audm")>;
+file out <single_file_mapper; file=arg("out")>;
+
+
+(file tio2auhm, file tio2audm, file out) = smeagol0_app (file au3dm, file au3hst, file aupsf,
+ file ausicpsf, file bulklft, file bulkrgt,
+ file inputfdf, file opsf, file osicpsf,
+ file tipsf, file tisicpsf);
+
Modified: SwiftApps/ematter/galaxy/smeagol0.xml
===================================================================
--- SwiftApps/ematter/galaxy/smeagol0.xml 2015-01-21 16:22:49 UTC (rev 8368)
+++ SwiftApps/ematter/galaxy/smeagol0.xml 2015-01-21 18:43:42 UTC (rev 8369)
@@ -1,31 +1,37 @@
-<tool id="swiftsmeagol_lead" name="smeagol lead swift">
+<tool id="swiftsmeagol0" name="smeagol0 swift">
<!--
ToDo:
1.
-->
- <description>A Galaxy tool to run the smeagol lead tool via Swift</description>
+ <description>A Galaxy tool to run the smeagol0 tool via Swift</description>
<command interpreter="python">
- swiftsmeagol_lead.py
+ swiftsmeagol0.py
+ "${_au3dm}"
+ "${_au3hst}"
"${_aupsf}"
"${_ausicpsf}"
+ "${_bulklft}"
+ "${_bulkrgt}"
"${_inputfdf}"
"${_opsf}"
"${_osicpsf}"
"${_tipsf}"
"${_tisicpsf}"
- "${_au3dm}"
- "${_au3hst}"
- "${_bulklft}"
- "${_bulkrgt}"
+ "${_tio2auhm}"
+ "${_tio2audm}"
"${_out}"
"${local_or_compute}"
</command>
<inputs>
+ <param name="_au3dm" size="30" type="data" label="au3dm" help="Select data for au3dm" />
+ <param name="_au3hst" size="30" type="data" label="au3hst" help="Select data for au3hst" />
<param name="_aupsf" size="30" type="data" label="aupsf" help="Select data for aupsf" />
<param name="_ausicpsf" size="30" type="data" label="ausicpsf" help="Select data for ausicpsf" />
+ <param name="bulklft" size="30" type="data" label="bulklft" help="Select data for bulklft" />
+ <param name="bulkrgt" size="30" type="data" label="bulkrgt" help="Select data for bulkrgt" />
<param name="_inputfdf" size="30" type="data" label="inputfdf" help="Select data for inputfdf" />
<param name="_opsf" size="30" type="data" label="opsf" help="Select data for opsf" />
<param name="_osicpsf" size="30" type="data" label="osicpsf" help="Select data for osicpsf" />
@@ -38,11 +44,9 @@
</param>
</inputs>
<outputs>
- <data format="txt" name="_au3dm" type="data" label="au3 DM output" />
- <data format="txt" name="_au3hst" type="data" label="au3 HST output" />
- <data format="txt" name="_bulklft" type="data" label="bulk left output" />
- <data format="txt" name="_bulkrgt" type="data" label="bulk right output" />
- <data format="txt" name="_out" type="data" label="smeagol lead output" />
+ <data format="txt" name="_tio2auhm" type="data" label="tio2auhm output" />
+ <data format="txt" name="_tio2audm" type="data" label="tio2audm output" />
+ <data format="txt" name="_out" type="data" label="smeagol0 output" />
</outputs>
<help>
@@ -51,16 +55,3 @@
</help>
</tool>
-<!--
-/* == Smeagol lead app definition == */
-app (file _au3dm, file _au3hst,
- file _bulklft, file _bulkrgt,
- file _out) smeagol_lead_app (file _aupsf, file _ausicpsf,
- file _inputfdf, file _opsf,
- file _osicpsf, file _tipsf,
- file _tisicpsf)
-{
- mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out;
-}
-
--->
Added: SwiftApps/ematter/galaxy/swiftsmeagol0.py
===================================================================
--- SwiftApps/ematter/galaxy/swiftsmeagol0.py (rev 0)
+++ SwiftApps/ematter/galaxy/swiftsmeagol0.py 2015-01-21 18:43:42 UTC (rev 8369)
@@ -0,0 +1,83 @@
+#!/usr/bin/env python
+
+"""
+This is the Swift driver for Galaxy. It receives inputs from the Swift
+Galaxy tool and depending on the options specified, builds a
+canonical Swift/K or Swift/T script and runs over specified computational
+environment.
+
+ swiftsmeagol0.py
+ "${_au3dm}"
+ "${_au3hst}"
+ "${_aupsf}"
+ "${_ausicpsf}"
+ "${_bulklft}"
+ "${_bulkrgt}"
+ "${_inputfdf}"
+ "${_opsf}"
+ "${_osicpsf}"
+ "${_tipsf}"
+ "${_tisicpsf}"
+ "${_tio2auhm}"
+ "${_tio2audm}"
+ "${_out}"
+ "${local_or_compute}"
+
+"""
+
+import subprocess
+import sys
+import os
+import distutils.spawn
+import traceback
+import fnmatch
+import re
+from os.path import expanduser
+
+def genargs(args):
+ for a in args:
+ yield a
+
+def main():
+ myargs = genargs(sys.argv)
+ try:
+ this=next(myargs)
+ au3dm = next(myargs)
+ au3hst = next(myargs)
+ aupsf = next(myargs)
+ ausicpsf = next(myargs)
+ bulklft = next(myargs)
+ bulkrgt = next(myargs)
+ inputfdf = next(myargs)
+ opsf = next(myargs)
+ osicpsf = next(myargs)
+ tipsf = next(myargs)
+ tisicpsf = next(myargs)
+ tio2auhm = next(myargs)
+ tio2audm = next(myargs)
+ out = next(myargs)
+ local_or_compute = next(myargs)
+ except:
+ traceback.print_exc()
+ sys.exit(1)
+
+ homedir = expanduser("~")
+
+ baseloc = homedir+"/SwiftApps/ematter/galaxy"
+
+ #which swift
+ swift = homedir+"/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift"
+ swiftargs="-au3dm="+au3dm+" -au3hst="+au3hst+" -aupsf="+aupsf+" -ausicpsf="+ausicpsf+" -bulklft="+bulklft+" -bulkrgt="+bulkrgt+" -inputfdf="+inputfdf+" -opsf="+opsf+" -osicpsf="+osicpsf+" -tipsf="+tipsf+" -tisicpsf="+tisicpsf+" -tio2auhm="+tio2auhm+" -tio2audm="+tio2audm+" -out="+out
+
+ siteval=baseloc+"/sites.local.xml"
+
+ if local_or_compute == "compute":
+ siteval=baseloc+"/sites.blues.xml"
+
+ #Invocation
+ exitcode=subprocess.check_call([swift, "-sites.file", siteval, "-tc.file", baseloc+"/apps", "-config", baseloc+"/cf", baseloc+"/smeagol0.swift", swiftargs])
+ #print exitcode
+
+if __name__=='__main__':
+ main()
+
Property changes on: SwiftApps/ematter/galaxy/swiftsmeagol0.py
___________________________________________________________________
Added: svn:executable
+ *
More information about the Swift-commit
mailing list