[Swift-commit] r6591 - in SwiftApps/strains: . midway

[davidk at ci.uchicago.edu]

Author: davidk
Date: 2013-07-01 11:33:46 -0500 (Mon, 01 Jul 2013)
New Revision: 6591

Added:
   SwiftApps/strains/midway/
   SwiftApps/strains/midway/FitPosOrStrains
   SwiftApps/strains/midway/clean.sh
   SwiftApps/strains/midway/sites.xml
   SwiftApps/strains/midway/strains.sh
   SwiftApps/strains/midway/strains.swift
   SwiftApps/strains/midway/tc.data
Log:
Strains swift script for midway


Added: SwiftApps/strains/midway/FitPosOrStrains
===================================================================
(Binary files differ)


Property changes on: SwiftApps/strains/midway/FitPosOrStrains
___________________________________________________________________
Added: svn:executable
   + *
Added: svn:mime-type
   + application/octet-stream

Added: SwiftApps/strains/midway/clean.sh
===================================================================
--- SwiftApps/strains/midway/clean.sh	                        (rev 0)
+++ SwiftApps/strains/midway/clean.sh	2013-07-01 16:33:46 UTC (rev 6591)
@@ -0,0 +1,3 @@
+#!/bin/bash -x
+
+rm -rf *.log *.rlog *.d *.kml *.swiftx SpotsToIndex*.csv FitBest_*.csv OrientPosIndexer_*.csv NrDiffIndexerFit_*.csv


Property changes on: SwiftApps/strains/midway/clean.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftApps/strains/midway/sites.xml
===================================================================
--- SwiftApps/strains/midway/sites.xml	                        (rev 0)
+++ SwiftApps/strains/midway/sites.xml	2013-07-01 16:33:46 UTC (rev 6591)
@@ -0,0 +1,13 @@
+<config>
+  <pool handle="midway-westmere">
+    <execution provider="coaster" jobmanager="local:slurm"/>
+    <profile namespace="globus" key="jobsPerNode">12</profile>
+    <profile namespace="globus" key="maxWalltime">00:10:00</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="globus" key="queue">bigmem</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}</workdirectory>
+  </pool>
+</config>

Added: SwiftApps/strains/midway/strains.sh
===================================================================
--- SwiftApps/strains/midway/strains.sh	                        (rev 0)
+++ SwiftApps/strains/midway/strains.sh	2013-07-01 16:33:46 UTC (rev 6591)
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+cat SpotsToIndex.*.csv > SpotsToIndex.csv
+/home/davidkelly999/strains/bin/run_FitPosOrStrains.sh /software/matlab-2012a-x86_64


Property changes on: SwiftApps/strains/midway/strains.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftApps/strains/midway/strains.swift
===================================================================
--- SwiftApps/strains/midway/strains.swift	                        (rev 0)
+++ SwiftApps/strains/midway/strains.swift	2013-07-01 16:33:46 UTC (rev 6591)
@@ -0,0 +1,27 @@
+type file;
+
+app (file o, file e, file fb, file nrd, file ori) strains (file pos, file extra, file param, file spotsti)
+{
+   strains stdout=@o stderr=@e;
+}
+
+file extrainfo <"InputAllExtraInfoFittingAll.csv">;
+file params <"paramstest.txt">;
+
+int spots[] = readData("spots.txt");
+
+foreach i in spots {
+   file SpotsToIndex <single_file_mapper; file=@strcat("SpotsToIndex.", i, ".csv")>;
+   SpotsToIndex=writeData(i);
+
+   string spotlong = @strcut(@strcat("0000000", i), "([0-9]........$)");
+   file bestpos <single_file_mapper; file=@strcat("Output/BestPos_", spotlong, ".csv")>;
+   file fitbest <single_file_mapper; file=@strcat("Results/FitBest_", spotlong, ".csv")>;
+   file nrdiff <single_file_mapper; file=@strcat("Results/NrDiffIndexerFit_", spotlong, ".csv")>;
+   file orient <single_file_mapper; file=@strcat("Results/OrientPosIndexer_", spotlong, ".csv")>;
+
+   file olog <single_file_mapper; file=@strcat("o.", i, ".log")>;
+   file elog <single_file_mapper; file=@strcat("e.", i, ".log")>;
+   (olog, elog, fitbest, nrdiff, orient) = strains(bestpos, extrainfo, params, SpotsToIndex);
+}
+

Added: SwiftApps/strains/midway/tc.data
===================================================================
--- SwiftApps/strains/midway/tc.data	                        (rev 0)
+++ SwiftApps/strains/midway/tc.data	2013-07-01 16:33:46 UTC (rev 6591)
@@ -0,0 +1 @@
+midway-westmere strains /home/davidkelly999/strains/midway/strains.sh