[Swift-commit] r7147 - in SwiftApps/Swift-MapRed: . Paper blast
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Wed Oct 9 23:10:07 CDT 2013
Author: ketan
Date: 2013-10-09 23:10:07 -0500 (Wed, 09 Oct 2013)
New Revision: 7147
Added:
SwiftApps/Swift-MapRed/blast/
SwiftApps/Swift-MapRed/blast/blast.swift
SwiftApps/Swift-MapRed/blast/formatdbmapper.sh
SwiftApps/Swift-MapRed/blast/outputmapper.sh
SwiftApps/Swift-MapRed/blast/sites.xml
SwiftApps/Swift-MapRed/blast/splitmapper.sh
SwiftApps/Swift-MapRed/blast/tc.data
Modified:
SwiftApps/Swift-MapRed/Paper/swifthadoop.tex
Log:
adding blast
Modified: SwiftApps/Swift-MapRed/Paper/swifthadoop.tex
===================================================================
--- SwiftApps/Swift-MapRed/Paper/swifthadoop.tex 2013-10-09 15:07:42 UTC (rev 7146)
+++ SwiftApps/Swift-MapRed/Paper/swifthadoop.tex 2013-10-10 04:10:07 UTC (rev 7147)
@@ -625,14 +625,6 @@
In this context, the filepointer should be interpreted and the actual files it points
to should be fetched if not present locally.
- 3.
+3.
-
-
-
-
-
-
-
-
Added: SwiftApps/Swift-MapRed/blast/blast.swift
===================================================================
--- SwiftApps/Swift-MapRed/blast/blast.swift (rev 0)
+++ SwiftApps/Swift-MapRed/blast/blast.swift 2013-10-10 04:10:07 UTC (rev 7147)
@@ -0,0 +1,52 @@
+type fastaseq;
+type headerfile;
+type indexfile;
+type seqfile;
+
+type database
+{
+ headerfile phr;
+ indexfile pin;
+ seqfile psq;
+}
+
+type query;
+type output;
+
+string num_partitions=@arg("n", "8");
+string program_name=@arg("p", "blastp");
+fastaseq dbin <single_file_mapper;file=@arg("d", "database")>;
+query query_file <single_file_mapper;file=@arg("i", "sequence.seq")>;
+string expectation_value=@arg("e", "0.1");
+output blast_output_file <single_file_mapper;file=@arg("o", "output.html")>;
+string filter_query_sequence=@arg("F", "F");
+
+fastaseq partition[] <ext;exec="splitmapper.sh",n=num_partitions>;
+
+app (fastaseq out[]) split_database (fastaseq d, string n){
+ fastasplitn @filename(d) n;
+}
+
+app (database out) formatdb (fastaseq i){
+ formatdb "-i" @filename(i);
+}
+
+app (output o) blastapp(query i, fastaseq d, string p, string e, string f, database db){
+ blastall "-p" p "-i" @filename(i) "-d" @filename(d) "-o" @filename(o) "-e" e "-T" "-F" f;
+}
+
+app (output o) blastmerge(output o_frags[]){
+ blastmerge @filename(o) @filenames(o_frags);
+}
+
+partition=split_database(dbin, num_partitions);
+
+database formatdbout[] <ext; exec="formatdbmapper.sh",n=num_partitions>;
+output out[] <ext; exec="outputmapper.sh",n=num_partitions>;
+
+foreach part,i in partition {
+ formatdbout[i] = formatdb(part);
+ out[i]=blastapp(query_file, part, program_name, expectation_value, filter_query_sequence, formatdbout[i]);
+}
+
+blast_output_file=blastmerge(out);
Added: SwiftApps/Swift-MapRed/blast/formatdbmapper.sh
===================================================================
--- SwiftApps/Swift-MapRed/blast/formatdbmapper.sh (rev 0)
+++ SwiftApps/Swift-MapRed/blast/formatdbmapper.sh 2013-10-10 04:10:07 UTC (rev 7147)
@@ -0,0 +1,18 @@
+#!/bin/bash
+while [ $# -gt 0 ]; do
+ case $1 in
+ -n) n=$2;;
+ *) echo "$0: bad mapper args" 1>&2
+ exit 1;;
+ esac
+ shift 2
+done
+
+for i in $(seq 1 $n)
+do
+ printf "[%d].phr frag%03d.phr\n" $i $i;
+ printf "[%d].pin frag%03d.pin\n" $i $i;
+ printf "[%d].psq frag%03d.psq\n" $i $i;
+done
+
+
Property changes on: SwiftApps/Swift-MapRed/blast/formatdbmapper.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/Swift-MapRed/blast/outputmapper.sh
===================================================================
--- SwiftApps/Swift-MapRed/blast/outputmapper.sh (rev 0)
+++ SwiftApps/Swift-MapRed/blast/outputmapper.sh 2013-10-10 04:10:07 UTC (rev 7147)
@@ -0,0 +1,16 @@
+#!/bin/bash
+while [ $# -gt 0 ]; do
+ case $1 in
+ -n) n=$2;;
+ *) echo "$0: bad mapper args" 1>&2
+ exit 1;;
+ esac
+ shift 2
+done
+
+for i in $(seq 1 $n)
+do
+ printf "[%d] frag%03d.html\n" $i $i;
+done
+
+
Property changes on: SwiftApps/Swift-MapRed/blast/outputmapper.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/Swift-MapRed/blast/sites.xml
===================================================================
--- SwiftApps/Swift-MapRed/blast/sites.xml (rev 0)
+++ SwiftApps/Swift-MapRed/blast/sites.xml 2013-10-10 04:10:07 UTC (rev 7147)
@@ -0,0 +1,23 @@
+<config>
+ <pool handle="localhost" sysinfo="INTEL32::LINUX">
+ <gridftp url="local://localhost" />
+ <execution provider="local" url="none" />
+ <workdirectory>/home/lgadelha/swiftwork</workdirectory>
+ <!-- <profile namespace="karajan" key="maxSubmitRate">1</profile> -->
+ <profile namespace="karajan" key="jobThrottle">0.03</profile>
+ <profile namespace="swift" key="stagingMethod">file</profile>
+ </pool>
+
+
+ <pool handle="sge-local">
+ <gridftp url="local://localhost" />
+ <execution provider="sge" url="localhost" />
+ <profile namespace="globus" key="pe">mpi1</profile>
+ <profile namespace="globus" key="queue">linux.q</profile>
+ <profile key="jobThrottle" namespace="karajan">6.23</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <filesystem provider="local" url="none" />
+ <workdirectory>/prj/prjssi/lgadelha/swiftwork</workdirectory>
+ </pool>
+</config>
+
Added: SwiftApps/Swift-MapRed/blast/splitmapper.sh
===================================================================
--- SwiftApps/Swift-MapRed/blast/splitmapper.sh (rev 0)
+++ SwiftApps/Swift-MapRed/blast/splitmapper.sh 2013-10-10 04:10:07 UTC (rev 7147)
@@ -0,0 +1,14 @@
+#!/bin/bash
+while [ $# -gt 0 ]; do
+ case $1 in
+ -n) n=$2;;
+ *) echo "$0: bad mapper args" 1>&2
+ exit 1;;
+ esac
+ shift 2
+done
+for i in $(seq 1 $n)
+do
+ printf "[%d] frag%03d\n" $i $i;
+done
+
Property changes on: SwiftApps/Swift-MapRed/blast/splitmapper.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/Swift-MapRed/blast/tc.data
===================================================================
--- SwiftApps/Swift-MapRed/blast/tc.data (rev 0)
+++ SwiftApps/Swift-MapRed/blast/tc.data 2013-10-10 04:10:07 UTC (rev 7147)
@@ -0,0 +1,27 @@
+#This is the transformation catalog.
+#
+#It comes pre-configured with a number of simple transformations with
+#paths that are likely to work on a linux box. However, on some systems,
+#the paths to these executables will be different (for example, sometimes
+#some of these programs are found in /usr/bin rather than in /bin)
+#
+#NOTE WELL: fields in this file must be separated by tabs, not spaces; and
+#there must be no trailing whitespace at the end of each line.
+#
+# sitename transformation path INSTALLED platform profiles
+localhost echo /bin/echo INSTALLED INTEL32::LINUX null
+localhost cat /bin/cat INSTALLED INTEL32::LINUX null
+localhost ls /bin/ls INSTALLED INTEL32::LINUX null
+localhost grep /bin/grep INSTALLED INTEL32::LINUX null
+localhost sort /bin/sort INSTALLED INTEL32::LINUX null
+localhost paste /bin/paste INSTALLED INTEL32::LINUX null
+localhost cp /bin/cp INSTALLED INTEL32::LINUX null
+localhost touch /bin/touch INSTALLED INTEL32::LINUX null
+localhost wc /usr/bin/wc INSTALLED INTEL32::LINUX null
+localhost sleep /bin/sleep null null null
+localhost blastall /opt/local/bin/blastall null null null
+localhost fastasplitn /Users/lgadelha/parallelblast/fastasplitn null null null
+localhost blastmerge /Users/lgadelha/parallelblast/blastmerge null null null
+localhost formatdb /opt/local/bin/formatdb null null null
+
+
More information about the Swift-commit
mailing list