[Swift-commit] r7327 - SwiftApps/Swift-MapRed/mapred_combiner_V4

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2013-11-25 09:55:55 -0600 (Mon, 25 Nov 2013)
New Revision: 7327

Modified:
   SwiftApps/Swift-MapRed/mapred_combiner_V4/blastreduce.swift
   SwiftApps/Swift-MapRed/mapred_combiner_V4/clean.sh
Log:
blast reduce

Modified: SwiftApps/Swift-MapRed/mapred_combiner_V4/blastreduce.swift
===================================================================
--- SwiftApps/Swift-MapRed/mapred_combiner_V4/blastreduce.swift	2013-11-25 15:51:33 UTC (rev 7326)
+++ SwiftApps/Swift-MapRed/mapred_combiner_V4/blastreduce.swift	2013-11-25 15:55:55 UTC (rev 7327)
@@ -39,7 +39,7 @@
  loc_bash @wrapper @reducer cmd @site_results stdout=@out stderr=@err;
 }
 
-string num_partitions = arg("n", "50");
+string num_partitions = arg("n", "200");
 fastaseq partition[] <ext;exec = "examples/blast/splitmapper.sh", n = num_partitions>;
 database formatdbout[] <ext; exec = "examples/blast/formatdbmapper.sh", n = num_partitions>;
 
@@ -52,7 +52,7 @@
 fileptr map_out[] <simple_mapper; prefix="map", suffix=".out">;
 file  map_err[] <simple_mapper; prefix="map", suffix=".err">;
 
-fastaseq dbin <single_file_mapper;file = arg("d", "/home/maheshwari/Swift-MapRed/blast/nr")>;
+fastaseq dbin <single_file_mapper;file = arg("d", "/scratch/midway/maheshwari/nr")>;
 query query_file <single_file_mapper;file = arg("i", "examples/blast/sequence.seq")>;
 
 partition=split_database(dbin, num_partitions);

Modified: SwiftApps/Swift-MapRed/mapred_combiner_V4/clean.sh
===================================================================
--- SwiftApps/Swift-MapRed/mapred_combiner_V4/clean.sh	2013-11-25 15:51:33 UTC (rev 7326)
+++ SwiftApps/Swift-MapRed/mapred_combiner_V4/clean.sh	2013-11-25 15:55:55 UTC (rev 7327)
@@ -7,4 +7,4 @@
 rm final_errors final_result       &> /dev/null
 rm exec_client exec_server         &> /dev/null
 rm -rf blastreduce-*-* swiftreduce-*-* &> /dev/null
-
+rm -rf frag* &> /dev/null