[Swift-commit] r8323 - SwiftApps/dsp-swift/galaxy
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Wed Dec 10 20:28:05 CST 2014
Author: ketan
Date: 2014-12-10 20:28:05 -0600 (Wed, 10 Dec 2014)
New Revision: 8323
Modified:
SwiftApps/dsp-swift/galaxy/swiftjumpdsp.py
SwiftApps/dsp-swift/galaxy/swiftjumpdsp.xml
Log:
gal
Modified: SwiftApps/dsp-swift/galaxy/swiftjumpdsp.py
===================================================================
--- SwiftApps/dsp-swift/galaxy/swiftjumpdsp.py 2014-12-11 01:06:49 UTC (rev 8322)
+++ SwiftApps/dsp-swift/galaxy/swiftjumpdsp.py 2014-12-11 02:28:05 UTC (rev 8323)
@@ -5,6 +5,15 @@
"foreach" Galaxy tool and depending on the options specified, builds a
canonical Swift/K or Swift/T script and runs over specified computational
environment.
+
+swiftjumpdsp.py
+ "${inlocation}"
+ "${a}"
+ "${n}"
+ "${p}"
+ "${I}"
+ "${outlist}"
+
"""
import subprocess
@@ -36,29 +45,14 @@
myargs = genargs(sys.argv)
try:
this=next(myargs)
- range_or_list = next(myargs)
- k_or_t = next(myargs)
- sites = next(myargs)
- swiftargs = next(myargs)
- interpreter = next(myargs)
- executable = next(myargs)
- stdin = next(myargs)
-
- if range_or_list == "list":
- #list of items
- listfile = next(myargs)
- n = sum(1 for line in open(listfile))
- else:
- # numeric range
- rstart = next(myargs)
- rend = next(myargs)
- stepsize = next(myargs)
- n = (int(rend) - int(rstart))/int(stepsize)
-
+ inloc = next(myargs)
+ a = next(myargs)
+ n = next(myargs)
+ p = next(myargs)
+ I = next(myargs)
outloc = next(myargs)
outlistfile = next(myargs)
logfile = next(myargs)
- stringargs = next(myargs)
except:
traceback.print_exc()
sys.exit(1)
Modified: SwiftApps/dsp-swift/galaxy/swiftjumpdsp.xml
===================================================================
--- SwiftApps/dsp-swift/galaxy/swiftjumpdsp.xml 2014-12-11 01:06:49 UTC (rev 8322)
+++ SwiftApps/dsp-swift/galaxy/swiftjumpdsp.xml 2014-12-11 02:28:05 UTC (rev 8323)
@@ -8,66 +8,16 @@
5. Add ability to run Swift/T.
6. Let the localhost option be selected by default
-->
- <description>A generic tool to run executable via Swift foreach parallel construct</description>
+ <description>A Galaxy tool to run Dsp parameter sweeps via Swift foreach parallel construct</description>
<command interpreter="python">
- #if $rangeorlist.rl == "rng"
- swiftforeach.py
- "range"
- "${k_or_t}"
- "${site}"
- "${swiftargs}"
- "${interpret}"
- "${exec}"
- "${stdin}"
- "${rangeorlist.rngstart}"
- "${rangeorlist.rend}"
- "${rangeorlist.stepsize}"
- "${outloc}"
- "${logfile}"
+ swiftjumpdsp.py
+ "${inlocation}"
+ "${a}"
+ "${n}"
+ "${p}"
+ "${I}"
"${outlist}"
- "${stringargs}"
- #for $a in $filearg
- ${a.fileargname}
- #end for
- #elif $rangeorlist.rl == "lst"
- swiftforeach.py
- "list"
- "${k_or_t}"
- "${site}"
- "${swiftargs}"
- "${interpret}"
- "${exec}"
- "${stdin}"
- "${rangeorlist.listfile}"
- "${outloc}"
- "${logfile}"
- "${outlist}"
- "${stringargs}"
- #for $a in $filearg
- ${a.fileargname}
- #end for
- #else
- swiftforeach.py
- "drytest"
- "${k_or_t}"
- "${site}"
- "${swiftargs}"
- "${interpret}"
- "${exec}"
- "${stdin}"
- "${rangeorlist.rngstart}"
- "${rangeorlist.rend}"
- "${rangeorlist.stepsize}"
- "${rangeorlist.listfile}"
- "${outloc}"
- "${logfile}"
- "${outlist}"
- "${stringargs}"
- #for $a in $filearg
- ${a.fileargname}
- #end for
- #end if
</command>
<!--
#if $swiftargs.mode == "advanced"
@@ -77,76 +27,15 @@
#end if
-->
<inputs>
- <param name="k_or_t" type="select" display="radio" label="choose target execution engine">
- <option value="swiftK" selected="true">Swift/K</option>
- <option value="swiftT" >Swift/T</option>
- </param>
-
- <param name="site" type="select" multiple="true" label="Execution Location" help="Multi-select list - NOTE: Swift/T option currently supports one site">
- <option value="localhost" selected="true">Localhost</option>
- <option value="midway">Midway</option>
- <option value="blues">Blues</option>
- <option value="uc3">UC3</option>
- <option value="stampede">Stampede</option>
- <option value="tukey">Tukey</option>
- <option value="vesta">Vesta</option>
- <option value="mira">Mira</option>
- </param>
-
- <param name="interpret" type="select" label="Execution interpreter">
- <option value="sh">sh</option>
- <option value="python">python</option>
- <option value="java">java</option>
- <option value="R">R</option>
- <option value="matlab">matlab</option>
- </param>
-
- <!--<param format="sh,binexec" name="exec" type="data" label="Executable"/>-->
- <param name="exec" type="data" label="Executable" help="select executable" />
-
- <param name="stdin" type="data" label="Standard input file" optional="true" help="select standard input" />
-
- <conditional name="rangeorlist">
- <param name="rl" type="select" label="Select range or list">
- <option value="rng">numeric range</option>
- <option value="lst">items list</option>
- <option value="tst">dry test</option>
- </param>
-
- <when value="rng">
- <param name="rngstart" size="2" type="integer" value="0" label="start"/>
- <param name="rend" size="2" type="integer" value="9" label="end"/>
- <param name="stepsize" size="2" type="integer" value="1" label="stepsize"/>
- </when>
-
- <when value="lst">
- <param format="data" name="listfile" type="data" label="List file" help="Select list file"/>
- </when>
-
- <when value="tst">
- <param name="rngstart" size="2" type="integer" value="0" label="start"/>
- <param name="rend" size="2" type="integer" value="9" label="end"/>
- <param name="stepsize" size="2" type="integer" value="1" label="stepsize"/>
- <param format="data" name="listfile" type="data" label="List file"/>
- </when>
-
- </conditional>
-
- <param name="stringargs" size="60" type="text" label="stringargs" help="Add application call commandline arguments here" />
-
- <repeat name="filearg" title="file arg">
- <param name="fileargname" type="data" label="filearg" />
- </repeat>
-
- <param name="swiftargs" size="60" type="text" label="swiftargs" help="Add Swift level commandline arguments" />
-
- <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>
+ <param name="inlocation" size="60" type="text" label="inlocation" help="Enter the path of the directory containing input data, eg. /home/ketan/farmer" />
+ <param name="a" size="60" type="text" label="aval" help="Enter the value of a"/>
+ <param name="n" size="60" type="text" label="nval" help="Enter the value of n"/>
+ <param name="p" size="60" type="text" label="pval" help="Enter the value of p"/>
+ <param name="I" size="60" type="text" label="Ival" help="Enter the value of I"/>
</inputs>
<outputs>
- <data format="txt" name="logfile" type="data" label="Swift output" />
- <data format="txt" name="outlist" type="data" label="Output list" />
+ <data format="txt" name="logfile" type="data" label="Application Output" />
+ <data format="txt" name="outlist" type="data" label="Output List" />
</outputs>
<!--
@@ -164,31 +53,7 @@
**What it does**
-This is a generic Swift tool that runs an executable in parallel over a range of numbers or a list of items from a file.
+This is a tool to run dsp via Swift in parallel over files provided by user.
-Execution location allows user to declare where to run the tool. Executable can be any arbitrary executable uploaded by user.
-
-Start, end, and stepsize are integer values. Note that the stepsize cannot be
-less than 1. Optionally, user can add new arguments to be provided to the tool
-executable after the numeric argument.
-
------
-
-**Example**
-
-Pick up an executable from the Executable list. Enter the start, end and the step size values. Enter an additional argument "hello".
-
-If an executable is echo.sh with following line:
-
-echo $@
-
-The start, end and step is 0, 9 and 2, the executable will be invoked in parallel 5 times for n where n is 0 2 4 6 8:
-
-echo n hello
-
------
-
-For more help, see: http://swift-lang.org/tutorials/galaxy/tutorial.html
-
</help>
</tool>
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