[Swift-commit] r7411 - SwiftApps/Blast/v2
wilde at ci.uchicago.edu
wilde at ci.uchicago.edu
Wed Dec 11 12:26:31 CST 2013
Author: wilde
Date: 2013-12-11 12:26:31 -0600 (Wed, 11 Dec 2013)
New Revision: 7411
Added:
SwiftApps/Blast/v2/mcs-local.properties
SwiftApps/Blast/v2/mcs-servers.properties
Removed:
SwiftApps/Blast/v2/apps
SwiftApps/Blast/v2/sites.local.xml
Modified:
SwiftApps/Blast/v2/blast2.swift
SwiftApps/Blast/v2/fblastall.sh
SwiftApps/Blast/v2/swift.properties
Log:
Optimizations for speed and adjustments for 0.95 config.
Deleted: SwiftApps/Blast/v2/apps
===================================================================
--- SwiftApps/Blast/v2/apps 2013-12-11 17:26:15 UTC (rev 7410)
+++ SwiftApps/Blast/v2/apps 2013-12-11 18:26:31 UTC (rev 7411)
@@ -1,18 +0,0 @@
-midway bash /bin/bash
-midway mid_bash /bin/bash
-midway loc_bash /bin/bash
-beagle bgl_bash /bin/bash
-local loc_bash /bin/bash
-local cat /bin/cat
-localhost bash bash
-midway blastmerge /root/parallelblast_2.0.9/blastmerge
-midway blastall /root/blast-2.2.26/bin/blastall
-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.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
-persistent-coasters blastall /root/blast-2.2.26/bin/blastall
-persistent-coasters blastmerge /root/parallelblast_2.0.9/blastmerge
Modified: SwiftApps/Blast/v2/blast2.swift
===================================================================
--- SwiftApps/Blast/v2/blast2.swift 2013-12-11 17:26:15 UTC (rev 7410)
+++ SwiftApps/Blast/v2/blast2.swift 2013-12-11 18:26:31 UTC (rev 7411)
@@ -3,16 +3,20 @@
type fasta;
type query;
-string num_partitions = arg("n", "10");
-string program_name = arg("p", "blastp");
-string expectation_value = arg("e", "0.1");
-string filter_query_sequence = arg("F", "F");
+string num_partitions = arg("n", "10");
+string blast_type = arg("p", "blastp");
+string expectation = arg("e", "0.1");
+string filter_query = arg("F", "F");
+string database = arg("d", "nr.sub1");
+string query = arg("q", "sequence.seq");
-fasta dbin <single_file_mapper;file=arg("d", "nr.sub1")>;
-query query_file <single_file_mapper;file=arg("i", "sequence.seq")>;
+tracef("database=%s\n", database);
-app (file dblist) split_database (fasta d, string n){
- 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;
+query query_file <single_file_mapper;file=query>;
+
+app (file dblist) split_database (string d, string n){
+ bash "-c" strcat("SPLITFRAGTEMPLATE=/tmp/db%3.3d fastasplitn ", 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){
@@ -23,14 +27,15 @@
blastmerge "-t" @o filenames(o_frags);
}
-file dbparts<"dbparts">;
-dbparts=split_database(dbin, num_partitions);
+file dbparts <"dbparts">;
+dbparts=split_database(database, num_partitions);
string db[] = readData(dbparts);
+trace(db);
file out[];
foreach partname,i in db {
fasta dbpart<single_file_mapper; file=partname>;
- out[i]=fblast(dbpart, query_file, program_name, expectation_value, filter_query_sequence);
+ out[i]=fblast(dbpart, query_file, blast_type, expectation, filter_query);
}
file merged <single_file_mapper;file=arg("o", "merged.txt")>;
Modified: SwiftApps/Blast/v2/fblastall.sh
===================================================================
--- SwiftApps/Blast/v2/fblastall.sh 2013-12-11 17:26:15 UTC (rev 7410)
+++ SwiftApps/Blast/v2/fblastall.sh 2013-12-11 18:26:31 UTC (rev 7411)
@@ -3,6 +3,9 @@
BLASTALL=/root/blast-2.2.26/bin/blastall
FORMAT=/root/blast-2.2.26/bin/formatdb
+BLASTALL=blastall
+FORMAT=formatdb
+
$FORMAT -i $1 -n $7
shift
Added: SwiftApps/Blast/v2/mcs-local.properties
===================================================================
--- SwiftApps/Blast/v2/mcs-local.properties (rev 0)
+++ SwiftApps/Blast/v2/mcs-local.properties 2013-12-11 18:26:31 UTC (rev 7411)
@@ -0,0 +1,34 @@
+site.local {
+ provider=local:local
+ jobsPerNode=1
+ maxWalltime=01:00:00
+ initialScore=10000
+ filesystem=local
+ workdirectory=/home/wilde/swiftwork
+ jobthrottle=0.1999
+}
+
+site=local
+
+# app.local.fastasplitn=/root/parallelblast_2.0.9/fastasplitn
+# app.local.formatdb=/root/blast-2.2.26/bin/formatdb
+# app.local.blastall=/root/blast-2.2.26/bin/blastall
+# app.local.fblastall=/root/blast.svn/v2/fblastall.sh
+# app.local.blastmerge=/root/parallelblast_2.0.9/blastmerge
+
+app.local.fastasplitn=fastasplitn
+app.local.formatdb=formatdb
+app.local.blastall=blastall
+app.local.fblastall=$HOME/swift/demo/blast/svn/v2/fblastall.sh
+app.local.blastmerge=blastmerge
+app.local.bash=bash
+
+use.provider.staging=true
+use.wrapper.staging=false
+wrapperlog.always.transfer=true
+execution.retries=0
+lazy.errors=false
+provider.staging.pin.swiftfiles=false
+sitedir.keep=true
+#tcp.port.range=50000,51000
+Dtcp.channel.log.io.performance=true
Added: SwiftApps/Blast/v2/mcs-servers.properties
===================================================================
--- SwiftApps/Blast/v2/mcs-servers.properties (rev 0)
+++ SwiftApps/Blast/v2/mcs-servers.properties 2013-12-11 18:26:31 UTC (rev 7411)
@@ -0,0 +1,44 @@
+
+site.local {
+ provider=local:local
+ jobsPerNode=1
+ maxWalltime=01:00:00
+ initialScore=10000
+# filesystem=local
+ workdirectory=/home/wilde/swiftwork
+ jobthrottle=0.1999
+}
+
+service.mcs {
+ jobsPerNode=4
+ jobThrottle=10
+ work=/home/wilde/swiftwork
+ workers=crush thwomp
+ mode=ssh
+}
+
+# app.local.fastasplitn=/root/parallelblast_2.0.9/fastasplitn
+# app.local.formatdb=/root/blast-2.2.26/bin/formatdb
+# app.local.blastall=/root/blast-2.2.26/bin/blastall
+# app.local.fblastall=/root/blast.svn/v2/fblastall.sh
+# app.local.blastmerge=/root/parallelblast_2.0.9/blastmerge
+
+#app.local.fastasplitn=fastasplitn
+#app.local.formatdb=formatdb
+#app.local.blastall=blastall
+
+site=local,mcs
+
+app.mcs.fblastall=/home/wilde/swift/demo/blast/svn/v2/fblastall.sh
+app.local.blastmerge=blastmerge
+app.local.bash=bash
+
+use.provider.staging=true
+use.wrapper.staging=false
+wrapperlog.always.transfer=true
+execution.retries=0
+lazy.errors=false
+provider.staging.pin.swiftfiles=false
+sitedir.keep=true
+#tcp.port.range=50000,51000
+Dtcp.channel.log.io.performance=true
Deleted: SwiftApps/Blast/v2/sites.local.xml
===================================================================
--- SwiftApps/Blast/v2/sites.local.xml 2013-12-11 17:26:15 UTC (rev 7410)
+++ SwiftApps/Blast/v2/sites.local.xml 2013-12-11 18:26:31 UTC (rev 7411)
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
- <pool handle="localhost">
- <execution provider="local" />
- <profile namespace="karajan" key="jobThrottle">0.01</profile>
- <profile namespace="karajan" key="initialScore">10000</profile>
- <filesystem provider="local"/>
- <workdirectory>swift.work</workdirectory>
- <profile namespace="swift" key="stagingMethod">local</profile>
- </pool>
-</config>
Modified: SwiftApps/Blast/v2/swift.properties
===================================================================
--- SwiftApps/Blast/v2/swift.properties 2013-12-11 17:26:15 UTC (rev 7410)
+++ SwiftApps/Blast/v2/swift.properties 2013-12-11 18:26:31 UTC (rev 7411)
@@ -1,3 +1,4 @@
+
site.local {
provider=local:local
jobsPerNode=1
@@ -3,17 +4,33 @@
maxWalltime=01:00:00
initialScore=10000
- filesystem=local
- workdirectory=/scratch/midway/$USER/work
+# filesystem=local
+ workdirectory=/home/wilde/swiftwork
jobthrottle=0.1999
}
-site=local
+service.mcs {
+ jobsPerNode=4
+ jobThrottle=10
+ work=/home/wilde/swiftwork
+ workers=crush thwomp
+ mode=ssh
+}
-app.local.fastasplitn=/root/parallelblast_2.0.9/fastasplitn
-app.local.formatdb=/root/blast-2.2.26/bin/formatdb
-app.local.blastall=/root/blast-2.2.26/bin/blastall
-app.local.fblastall=/root/blast.svn/v2/fblastall.sh
-app.local.blastmerge=/root/parallelblast_2.0.9/blastmerge
+# app.local.fastasplitn=/root/parallelblast_2.0.9/fastasplitn
+# app.local.formatdb=/root/blast-2.2.26/bin/formatdb
+# app.local.blastall=/root/blast-2.2.26/bin/blastall
+# app.local.fblastall=/root/blast.svn/v2/fblastall.sh
+# app.local.blastmerge=/root/parallelblast_2.0.9/blastmerge
+#app.local.fastasplitn=fastasplitn
+#app.local.formatdb=formatdb
+#app.local.blastall=blastall
+
+site=local,mcs
+
+app.mcs.fblastall=$HOME/swift/demo/blast/svn/v2/fblastall.sh
+app.local.blastmerge=blastmerge
+app.local.bash=bash
+
use.provider.staging=true
use.wrapper.staging=false
More information about the Swift-commit
mailing list