Commit c833907a authored by Olivier Langella's avatar Olivier Langella
Browse files

masschroq (2.0.1-4) wheezy

new masschroq-condor package to install masschroq-condor perl script
parent 89ee9a77
......@@ -130,7 +130,6 @@ SET(CPACK_SOURCE_IGNORE_FILES
".*\\\\.toc"
"/devel_archives/"
"/doc\\\\/misc/"
"/doc\\\\/scripts/"
"/doc\\\\/slides/"
"/doc\\\\/examples/"
"/figures/"
......@@ -146,7 +145,7 @@ SET(CPACK_SOURCE_IGNORE_FILES
"/Release/"
"/tests/"
"/\\\\.externalToolBuilders/"
"/\\\\.svn/"
"/\\\\.git/"
"/\\\\.settings/"
"Makefile"
"\\\\.cdtbuild"
......@@ -184,6 +183,8 @@ SET(CPACK_SOURCE_IGNORE_FILES
MESSAGE("configuring file ${masschroq_SOURCE_DIR}/src/config.h.cmake")
configure_file (${masschroq_SOURCE_DIR}/src/config.h.cmake ${masschroq_SOURCE_DIR}/src/config.h)
configure_file (${CMAKE_SOURCE_DIR}/doc/scripts/masschroq-condor.pl ${CMAKE_BINARY_DIR}/src/masschroq-condor.pl @COPYONLY)
configure_file (${CMAKE_SOURCE_DIR}/doc/scripts/masschroq-split.py ${CMAKE_BINARY_DIR}/src/masschroq-split.py @COPYONLY)
......@@ -212,6 +213,7 @@ add_subdirectory (src)
INSTALL(PROGRAMS ${masschroq_BINARY_DIR}/src/masschroq DESTINATION bin)
INSTALL(PROGRAMS ${masschroq_BINARY_DIR}/src/masschroq_gui DESTINATION bin)
INSTALL(PROGRAMS ${masschroq_BINARY_DIR}/src/masschroq_studio DESTINATION bin)
INSTALL(PROGRAMS ${masschroq_BINARY_DIR}/src/masschroq-condor.pl DESTINATION bin)
INSTALL(FILES ${masschroq_SOURCE_DIR}/doc/schema/${MASSCHROQ_SCHEMA_FILE} DESTINATION share/xml/schema)
INSTALL(FILES ${masschroq_SOURCE_DIR}/doc/logo/masschroq.svg DESTINATION share/masschroq)
INSTALL(FILES ${masschroq_SOURCE_DIR}/templates/share/applications/masschroq-gui.desktop DESTINATION share/applications)
......
masschroq (2.0.1-4) wheezy; urgency=low
* new sub package to install the masschroq-condor.pl perl script
-- Olivier Langella <Olivier.Langella@moulon.inra.fr> Thu, 19 Sep 2013 08:18:51 +0200
masschroq (2.0.1-3) wheezy; urgency=low
* debian wheezy package
......
......@@ -68,3 +68,10 @@ Description: Mass Chromatogram Quantification graphical user interface to edit p
In particular it performs : retention-time alignment of runs, XIC extraction and filtering,
peak detection and quantification.
Package: masschroq-condor
Architecture: all
Depends: ${shlibs:Depends}, masschroq, condor
Suggests: masschroq-doc, masschroq-gui, masschroq-studio
Description: Perl script to launch MassChroQ via condor job queue
Perl script to launch MassChroQ via condor job queue
/usr/bin/masschroq-condor.pl
\ No newline at end of file
......@@ -32,7 +32,7 @@ open my $condor_file,
print $condor_file "Universe = vanilla\n";
print $condor_file "Executable = /usr/bin/masschroq\n";
print $condor_file "Executable = ${CMAKE_INSTALL_PREFIX}/bin/masschroq\n";
print $condor_file "Log = $tempdir/submit_condor.log\n";
......@@ -52,8 +52,8 @@ print $condor_file "Queue\n";
close $condor_file;
print "Created masschroq condor submission file submit_condor_masschroq.txt\n";
print "Created condor job temporary directory $tempdir\n";
print "masschroq condor submission file submit_condor_masschroq.txt created\n";
print "condor job temporary directory $tempdir created\n";
# help function
sub display_help {
......
#!/usr/bin/python
import argparse
import sys
import os
#Defined command line
desc = 'Splits a MassChroQml file into small pieces in a subdirectory.'
command = argparse.ArgumentParser(prog='mcq-split', \
description=desc, usage='%(prog)s [options]')
command.add_argument('-i', '--infile', \
type=argparse.FileType("r"), \
help='Open a MassChroQml file', required=True)
command.add_argument('-v', '--version', action='version', \
version='%(prog)s ${MASSCHROQ_VERSION}')
#Read arguments of command line
args = command.parse_args()
sys.stderr.write("input file is :'" + args.infile.name + "'\n")
mcqmlFile = args.infile
mcqmlSplitDir = args.infile.name + '.d'
if not os.path.exists(mcqmlSplitDir) :
os.mkdir(mcqmlSplitDir)
os.system('xmlstarlet sel -t -c "/masschroq/rawdata" '+mcqmlFile.name+' > '+mcqmlSplitDir+'/rawdata.xml')
#masschroq/groups
os.system('xmlstarlet sel -t -c "/masschroq/groups" '+mcqmlFile.name+' > '+mcqmlSplitDir+'/groups.xml')
#masschroq/align
os.system('xmlstarlet sel -t -c "/masschroq/align" '+mcqmlFile.name+' > '+mcqmlSplitDir+'/align.xml')
#masschroq/quantification_methods
os.system('xmlstarlet sel -t -c "/masschroq/quantification_methods" '+mcqmlFile.name+' > '+mcqmlSplitDir+'/quantification_methods.xml')
#masschroq/quantification/quantification_results
os.system('xmlstarlet sel -t -c "/masschroq/quantification/quantification_results" '+mcqmlFile.name+' > '+mcqmlSplitDir+'/quantification_results.xml')
#masschroq/quantification/quantification_traces
os.system('xmlstarlet sel -t -c "/masschroq/quantification/quantification_traces" '+mcqmlFile.name+' > '+mcqmlSplitDir+'/quantification_traces.xml')
xmlstarlet el "/masschroq/rawdata" /gorgone/pappso/moulon/users/Olivier/ludovic/B73_Complet_V3-1-0.masschroqML
xmlstarlet sel -t -c "/masschroq/rawdata" /gorgone/pappso/moulon/users/Olivier/ludovic/B73_Complet_V3-1-0.masschroqML > /tmp/data_files.xml
xmlstarlet ed -d "/masschroq/rawdata" /gorgone/pappso/moulon/users/Olivier/ludovic/B73_Complet_V3-1-0.masschroqML > /tmp/sans_data.xml
xmlstarlet tr --xinclude /tmp/test.xsl /tmp/inc.xml
xmlstarlet ed -i "/masschroq" -t attr -n "xmlns:xi" -v "http://www.w3.org/2001/XInclude" /tmp/sans_data.xml > /tmp/attr.xml
xmlstarlet ed -i "/masschroq/groups" -t elem -n "xi:include" -v "" -i "/masschroq/include" -t attr -n "href" -v "data_files.xml" /tmp/attr.xml > /tmp/sans.xml
xmlstarlet ed -i "/masschroq/xi:include" -t attr -n "href" -v "data_files.xml" /tmp/sans.xml > /tmp/inc.xml
<xsl:stylesheet version="2.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:fo="http://www.w3.org/1999/XSL/Format" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:fn="http://www.w3.org/2005/xpath-functions">
<xsl:template match="/">
<xsl:copy-of select="."/>
</xsl:template>
</xsl:stylesheet>
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