[Swift-commit] r7402 - SwiftApps/Blast/v2

[wilde at ci.uchicago.edu]

Author: wilde
Date: 2013-12-10 23:11:32 -0600 (Tue, 10 Dec 2013)
New Revision: 7402

Modified:
   SwiftApps/Blast/v2/apps
   SwiftApps/Blast/v2/blast2.swift
Log:
Adjust fblastall shell location; add template for fastasplit output.

Modified: SwiftApps/Blast/v2/apps
===================================================================
--- SwiftApps/Blast/v2/apps	2013-12-11 04:50:42 UTC (rev 7401)
+++ SwiftApps/Blast/v2/apps	2013-12-11 05:11:32 UTC (rev 7402)
@@ -10,7 +10,7 @@
 localhost fastasplitn /root/parallelblast_2.0.9/fastasplitn
 localhost formatdb /root/blast-2.2.26/bin/formatdb
 localhost blastall /root/blast-2.2.26/bin/blastall
-localhost fblastall /root/blast.mw/fblastall.sh
+localhost fblastall /root/blast.svn/v2/fblastall.sh
 localhost blastmerge /root/parallelblast_2.0.9/blastmerge
 persistent-coasters fastasplitn /root/parallelblast_2.0.9/fastasplitn
 persistent-coasters formatdb /root/blast-2.2.26/bin/formatdb

Modified: SwiftApps/Blast/v2/blast2.swift
===================================================================
--- SwiftApps/Blast/v2/blast2.swift	2013-12-11 04:50:42 UTC (rev 7401)
+++ SwiftApps/Blast/v2/blast2.swift	2013-12-11 05:11:32 UTC (rev 7402)
@@ -12,7 +12,7 @@
 query  query_file <single_file_mapper;file=arg("i", "sequence.seq")>;
 
 app (file dblist) split_database (fasta d, string n){
-  bash "-c" strcat("/root/parallelblast_2.0.9/fastasplitn ", at d, " ", n, " 2>&1 | grep Opening | sed -e 's/^.* //'") stdout=@dblist;
+  bash "-c" strcat("SPLITFRAGTEMPLATE=/tmp/db%3.3d /root/parallelblast_2.0.9/fastasplitn ", at d, " ", n, " 2>&1 | grep Opening | sed -e 's/^.* //'") stdout=@dblist;
 }
 
 app (file o) fblast(fasta d, query i, string p, string e, string f){