[Swift-commit] r7226 - SwiftApps/Swift-MapRed/blast

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2013-10-24 14:58:22 -0500 (Thu, 24 Oct 2013)
New Revision: 7226

Added:
   SwiftApps/Swift-MapRed/blast/apps
Removed:
   SwiftApps/Swift-MapRed/blast/tc.data
Modified:
   SwiftApps/Swift-MapRed/blast/blast.swift
   SwiftApps/Swift-MapRed/blast/run.sh
Log:
 

Copied: SwiftApps/Swift-MapRed/blast/apps (from rev 7225, SwiftApps/Swift-MapRed/blast/tc.data)
===================================================================
--- SwiftApps/Swift-MapRed/blast/apps	                        (rev 0)
+++ SwiftApps/Swift-MapRed/blast/apps	2013-10-24 19:58:22 UTC (rev 7226)
@@ -0,0 +1,5 @@
+midway blastp /home/maheshwari/ncbi-blast-2.2.28+/bin/blastp
+midway fastasplitn /home/maheshwari/parallelblast_2.0.9/fastasplitn
+midway blastmerge /home/maheshwari/parallelblast_2.0.9/blastmerge
+midway blastall /home/maheshwari/blast-2.2.26/bin/blastall
+midway formatdb /home/maheshwari/blast-2.2.26/bin/formatdb

Modified: SwiftApps/Swift-MapRed/blast/blast.swift
===================================================================
--- SwiftApps/Swift-MapRed/blast/blast.swift	2013-10-24 19:48:56 UTC (rev 7225)
+++ SwiftApps/Swift-MapRed/blast/blast.swift	2013-10-24 19:58:22 UTC (rev 7226)
@@ -12,7 +12,7 @@
 type query;
 type output;
 
-string num_partitions=@arg("n", "8");
+string num_partitions=@arg("n", "50");
 string program_name=@arg("p", "blastp");
 fastaseq dbin <single_file_mapper;file=@arg("d", "nr")>;
 query query_file <single_file_mapper;file=@arg("i", "sequence.seq")>;

Modified: SwiftApps/Swift-MapRed/blast/run.sh
===================================================================
--- SwiftApps/Swift-MapRed/blast/run.sh	2013-10-24 19:48:56 UTC (rev 7225)
+++ SwiftApps/Swift-MapRed/blast/run.sh	2013-10-24 19:58:22 UTC (rev 7226)
@@ -1 +1 @@
-swift -sites.file sites.xml -config cf tc.file tc.data blast.swift
+swift -sites.file sites.xml -config cf -tc.file apps blast.swift

Deleted: SwiftApps/Swift-MapRed/blast/tc.data
===================================================================
--- SwiftApps/Swift-MapRed/blast/tc.data	2013-10-24 19:48:56 UTC (rev 7225)
+++ SwiftApps/Swift-MapRed/blast/tc.data	2013-10-24 19:58:22 UTC (rev 7226)
@@ -1,6 +0,0 @@
-localhost blastp /home/maheshwari/ncbi-blast-2.2.28+/bin/blastp
-localhost fastasplitn /home/maheshwari/parallelblast_2.0.9/fastasplitn
-localhost blastmerge /home/maheshwari/parallelblast_2.0.9/blastmerge
-#localhost formatdb /home/maheshwari/ncbi-blast-2.2.28+/bin/makeblastdb
-localhost blastall /home/maheshwari/blast-2.2.26/bin/blastall
-localhost formatdb /home/maheshwari/blast-2.2.26/bin/formatdb