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[Sashimi-commit] SF.net SVN: sashimi:[5119] trunk/trans_proteomic_pipeline/extern/hpctools/ grid/bin
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From: <sla...@us...> - 2010-08-24 22:43:30
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Revision: 5119
http://sashimi.svn.sourceforge.net/sashimi/?rev=5119&view=rev
Author: slagelwa
Date: 2010-08-24 22:43:24 +0000 (Tue, 24 Aug 2010)
Log Message:
-----------
Adding qmyrimatch
Supporting both mzXML and mzML files
Checking for resulting file in qconvert
Modified Paths:
--------------
trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qconvert
trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qgrid_functions
trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qomssa
Added Paths:
-----------
trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qmyrimatch
Modified: trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qconvert
===================================================================
--- trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qconvert 2010-08-24 21:04:39 UTC (rev 5118)
+++ trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qconvert 2010-08-24 22:43:24 UTC (rev 5119)
@@ -41,7 +41,7 @@
# QEND=${QEND-}
# Default remote convert flags
- REMOTECONVERTFLAGS=${REMOTECONVERTFLAGS-}
+ REMOTECONVERTFLAGS=${REMOTECONVERTFLAGS-}
# Programs
QSUB=${QSUB-`which qsub 2>/dev/null`}
@@ -71,13 +71,14 @@
# Write search commands to qsub script
#
function write_qsub {
+ rm -f $root.convert.qsub $root.convert.log
cat <<EOF > $1
$(qsub_header $root.convert.log)
log "CONVERT $input"
-$REMOTECONVERT $REMOTECONVERTFLAGS "$input"
-cat convert.log
-rm convert.log
+$REMOTECONVERT $REMOTECONVERTFLAGS --log2screen "$input"
+[ -f convert.log ] && cat convert.log
+rm -f convert.log
# Did it produce a file?
if [ ! -f "${input%.*}".mz*ML ]; then
Modified: trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qgrid_functions
===================================================================
--- trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qgrid_functions 2010-08-24 21:04:39 UTC (rev 5118)
+++ trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qgrid_functions 2010-08-24 22:43:24 UTC (rev 5119)
@@ -114,7 +114,7 @@
DEST="$2"
shift 2
;;
- *.mzML|*.mzXML|*.mzXML.gz)
+ *.mzML|*.mzXML|*.mzXML.gz|*.mgf)
[ -f "$1" ] || usage "Error $1 file not found";
INPUTS="$INPUTS $1"
shift
Added: trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qmyrimatch
===================================================================
--- trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qmyrimatch (rev 0)
+++ trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qmyrimatch 2010-08-24 22:43:24 UTC (rev 5119)
@@ -0,0 +1,97 @@
+#!/bin/bash
+#
+# Program: TPP HPC Tools
+# Author: Joe Slagel
+#
+# Copyright (C) 2009 by Joseph Slagel
+#
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 2.1 of the License, or (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+#
+# Institute for Systems Biology
+# 1441 North 34th St.
+# Seattle, WA 98103 USA
+# js...@sy...
+#
+# $Id: $
+#
+
+. qgrid_functions # Load grid functions
+
+
+# -- Local settings -----------------------------------------------------------
+
+ # What command tool are we
+ QJOBNAME=${QJOBNAME:-TPP-myrimatch}
+
+ # Submission log file
+ QLOG=${QLOG-/dev/null}
+
+ # Default queue to submit jobs to
+ QQUEUE=${QQUEUE-xtandem}
+
+ # Additional commands to run when exiting
+ #QEND=${QEND-}
+
+ # Parameters file
+ PARAMS=myrimatch.params
+
+ # Programs
+ QSUB=${QSUB-`which qsub 2>/dev/null`}
+ MYRIMATCH=${MYRIMATCH-`which myrimatch 2>/dev/null`}
+
+
+# -- Functions ----------------------------------------------------------------
+
+#
+# Write out a qsub script
+#
+function write_qsub {
+ cat <<EOF > $1
+$(qsub_header $root.myrimatch.log)
+
+log "START $input"
+
+$MYRIMATCH -cfg $PARAMS $input
+/regis/sbeams/bin/fixNon5DigitScanPepXML.pl $root.pepXML $root.pep.xml
+/bin/rm -f $root.pepXML
+
+${QEND}
+
+log "DONE $input"
+EOF
+}
+
+
+# -- Main ----------------------------------------------------------------------
+
+# Check for necessary programs
+[ ! -x ${QSUB} ] && usage "Error no qsub in your path"
+[ ! -x ${MYRIMATCH} ] && usage "Error no myrimatch in your path"
+search_input $*
+
+# Submit jobs
+for input in $INPUTS; do
+ input=$(rel2abs "$input") # use abs path
+ dir=$(dirname "$input") # base directory of input
+ root=$(basename "${input%.mz*ML*}") # filename w/o extension
+
+ rm -f $root.myrimatch.log # remove previous results
+ rm -f $root.pep.xml
+
+ write_qsub $root.myrimatch.qsub
+
+ log "SUBMIT $input"
+ $QSUB $root.myrimatch.qsub
+done
Property changes on: trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qmyrimatch
___________________________________________________________________
Added: svn:executable
+ *
Modified: trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qomssa
===================================================================
--- trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qomssa 2010-08-24 21:04:39 UTC (rev 5118)
+++ trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qomssa 2010-08-24 22:43:24 UTC (rev 5119)
@@ -97,8 +97,8 @@
dir=$(dirname $(rel2abs "$input")) # base directory of input
root=$(basename "${input%.mz*ML}") # filename w/o extension
- write_qsub "$root.qsub"
+ write_qsub "$root.omssa.qsub"
log "SUBMIT $input"
- $QSUB $dir/$root.qsub
+ $QSUB $dir/$root.omssa.qsub
done
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