Mercurial > repos > crs4 > sspace
changeset 1:93fa7ecb5292 draft
Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
| author | crs4 |
|---|---|
| date | Fri, 21 Feb 2014 04:17:55 -0500 |
| parents | b1be94418db9 |
| children | bc4451edb703 |
| files | COPYING readme.rst sspace.py sspace.xml tool_dependencies.xml |
| diffstat | 5 files changed, 46 insertions(+), 152 deletions(-) [+] |
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--- a/COPYING Tue Sep 17 09:41:18 2013 -0400 +++ b/COPYING Fri Feb 21 04:17:55 2014 -0500 @@ -1,4 +1,4 @@ -Copyright © 2012-2013 CRS4 Srl. http://www.crs4.it/ +Copyright © 2012-2014 CRS4 Srl. http://www.crs4.it/ Created by: Massimiliano Orsini <massimiliano.orsini@crs4.it> Gianmauro Cuccuru <gianmauro.cuccuru@crs4.it>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Fri Feb 21 04:17:55 2014 -0500 @@ -0,0 +1,28 @@ +SSPACE wrapper +============== + +Configuration +------------- + +sspace tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see https://wiki.galaxyproject.org/Admin/Config/Jobs and https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ). + +If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of CPU cores allocated by the job runner according to the configuration of the destination selected for this tool. + +If instead you are using an older Galaxy release, you should also add a line + + GALAXY_SLOTS=N; export GALAXY_SLOTS + +(where N is the number of CPU cores allocated by the job runner for this tool) to the file + + <tool_dependencies_dir>/sspace/2.0/crs4/sspace/<hash_string>/env.sh + +Version history +--------------- + +- Release 1: Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst . +- Release 0: Initial release in the Tool Shed. + +Development +----------- + +Development is hosted at https://bitbucket.org/crs4/orione-tools . Contributions and bug reports are very welcome!
--- a/sspace.py Tue Sep 17 09:41:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,129 +0,0 @@ -# -*- coding: utf-8 -*- -""" -SSPACE wrapper -""" - -import logging -import optparse -import os -import shutil -import subprocess -import tempfile - - -def which(name, flags=os.X_OK): - """ Search PATH for executable files with the given name. """ - result = [] - exts = filter(None, os.environ.get('PATHEXT', '').split(os.pathsep)) - path = os.environ.get('PATH', None) - if path is None: - return [] - for p in os.environ.get('PATH', '').split(os.pathsep): - p = os.path.join(p, str(name)) - if os.access(p, flags): - result.append(p) - for e in exts: - pext = p + e - if os.access(pext, flags): - result.append(pext) - return result - - -LOG_FORMAT = '%(asctime)s|%(levelname)-8s|%(message)s' -LOG_DATEFMT = '%Y-%m-%d %H:%M:%S' -LOG_LEVELS = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'] - - -def __main__(): - """ main function """ - parser = optparse.OptionParser() - parser.add_option('-c', dest='contigs', help='contigs mandatory (-s)') - parser.add_option('--r1', dest='reads1', help='') - parser.add_option('--r2', dest='reads2', help='') - parser.add_option('-i', dest='insert', type='int', help='') - parser.add_option('-e', dest='error', type='float', help='') - parser.add_option('-o', dest='orientation', choices=['FF', 'FR', 'RF', 'RR'], help='') - parser.add_option('-x', action='store_true', dest='extension', help='whether to extend the contigs (-x)') - parser.add_option('--minoverlap', dest='minoverlap', type='int', help='minoverlap (-m)') - parser.add_option('--numofreads', dest='numofreads', type='int', help='num of reads to call an extension (-o)') - parser.add_option('-t', dest='max_trim', type='int', help='maximum number of bases to trim on the contig end when all possibilities have been exhausted for an extension (-t)') - parser.add_option('-u', dest='unpaired', help='unpaired reads (-u, optional)') - parser.add_option('-r', dest='min_base_ratio', type='float', help='minimum base ratio used to accept a overhang consensus base (-r)') - parser.add_option('--minlink', dest='minlink', type='int', help='min link (-k)') - parser.add_option('--maxratio', dest='maxratio', type='float', help='max ratio (-a)') - parser.add_option('--contigoverlap', dest='contigoverlap', type='int', help='contigoverlap (-n)') - parser.add_option('--mincontig', dest='mincontig', type='int', help='mincontig (-z)') - parser.add_option('-T', dest='n_threads', type='int', help='number of threads to use in Bowtie (-T)') - parser.add_option('-p', dest='prefix', default='sspace_pre', help='prefix (-b)') - parser.add_option('--lib', dest='libraryname', default='galx', help='libraryfile') - parser.add_option('--fe', dest='finalevidence', help='') - parser.add_option('--fs', dest='finalscaffolds', help='') - parser.add_option('--lg', dest='logfile', help='') - parser.add_option('--summ', dest='summaryfile', help='') - parser.add_option('--loglevel', choices=LOG_LEVELS, help='logging level (default: INFO)', default='DEBUG') - (options, args) = parser.parse_args() - if len(args) > 0: - parser.error('Wrong number of arguments') - - log_level = getattr(logging, options.loglevel) - kwargs = {'format' : LOG_FORMAT, - 'datefmt' : LOG_DATEFMT, - 'level' : log_level} - if options.logfile: - kwargs['filename'] = options.logfile - logging.basicConfig(**kwargs) - logger = logging.getLogger('SSPACE scaffold assembly') - - logger.debug('Creating temp dir') - contigs = options.contigs - reads1 = options.reads1 - reads2 = options.reads2 - insert = options.insert - error = options.error - orientation = options.orientation - extension = '-x 1' if options.extension else '' - minoverlap = "-m %d" % options.minoverlap if options.minoverlap is not None else '' - numofreads = "-o %d" % options.numofreads if options.numofreads is not None else '' - max_trim = "-t %d" % options.max_trim if options.max_trim is not None else '' - unpaired = "-u %s" % options.unpaired if options.unpaired else '' - min_base_ratio = "-r %s" % options.min_base_ratio if options.min_base_ratio is not None else '' - minlink = "-k %d" % options.minlink if options.minlink is not None else '' - maxratio = "-a %s" % options.maxratio if options.maxratio is not None else '' - contigoverlap = "-n %d" % options.contigoverlap if options.contigoverlap is not None else '' - mincontig = "-z %d" % options.mincontig if options.mincontig is not None else '' - n_threads = "-T %d" % options.n_threads if options.n_threads is not None else '' - prefix = options.prefix - libraryname = options.libraryname - finalevidence = options.finalevidence - finalscaffolds = options.finalscaffolds - summaryfile = options.summaryfile - exe_name = "SSPACE_Basic_v2.0.pl" - - # Set library - outline = 'lib1 %s %s %d %s %s\n' % (reads1, reads2, insert, error, orientation) - with open(libraryname, 'w') as out: - out.write(outline) - - exe = which(exe_name, os.R_OK) - command = "perl %s -l %s -s %s %s %s %s %s %s %s %s %s %s %s %s -b %s" % (exe.pop(), libraryname, contigs, extension, minoverlap, numofreads, max_trim, unpaired, min_base_ratio, minlink, maxratio, contigoverlap, mincontig, n_threads, prefix) - wd = tempfile.mkdtemp() - try: - os.chdir(wd) - logger.info("SSPACE running") - logger.debug("executing %s" % command) - subprocess.check_call(args=command, shell=True) - - # Clean environment - with open("%s.logfile.txt" % os.path.join(wd, prefix), 'rb') as sspace_log_file: - logger.info("\n".join(["Log from SSPACE", sspace_log_file.read()])) - logger.info("Moving result files") - shutil.move("%s.final.evidence" % os.path.join(wd, prefix), finalevidence) - shutil.move("%s.final.scaffolds.fasta" % os.path.join(wd, prefix), finalscaffolds) - shutil.move("%s.summaryfile.txt" % os.path.join(wd, prefix), summaryfile) - logger.debug("Removing temp dir: %s" % wd) - finally: - shutil.rmtree(wd) - - -if __name__ == "__main__": - __main__()
--- a/sspace.xml Tue Sep 17 09:41:18 2013 -0400 +++ b/sspace.xml Fri Feb 21 04:17:55 2014 -0500 @@ -1,21 +1,20 @@ -<tool id="sspace" name="SSPACE" version="1.0.5"> +<tool id="sspace" name="SSPACE" version="1.0.6"> <description>scaffolder</description> <requirements> <requirement type="package" version="2.0">sspace</requirement> </requirements> - <command interpreter="python"> - sspace.py - \${SSPACE_SITE_OPTIONS:--T 1} - -c $contigs --r1 $reads1 --r2 $reads2 -i $insert -e $error -o $orientation + <command> + echo "lib1 $reads1 $reads2 $insert $error $orientation" > libraryfile && + perl `which SSPACE_Basic_v2.0.pl` -l libraryfile -s $contigs #if $exten - -x + -x 1 #end if #if str($minoverlap) - --minoverlap $minoverlap + -m $minoverlap #end if #if str($numofreads) - --numofreads $numofreads + -o $numofreads #end if #if str($max_trim) -t $max_trim @@ -27,18 +26,18 @@ -r $min_base_ratio #end if #if str($minlink) - --minlink $minlink + -k $minlink #end if #if str($maxratio) - --maxratio $maxratio + -a $maxratio #end if #if str($contigoverlap) - --contigoverlap $contigoverlap + -n $contigoverlap #end if #if str($mincontig) - --mincontig $mincontig + -z $mincontig #end if - --lib $libraryname --fe $finalevidence --fs $finalscaffolds --lg $logfile --summ $summaryfile + -T \${GALAXY_SLOTS:-1} -b sspace </command> <inputs> @@ -78,11 +77,10 @@ </inputs> <outputs> - <data name="libraryname" hidden="True" format="tabular" label="${tool.name} on ${on_string}: libraryfile" /> - <data name="finalevidence" format="txt" label="${tool.name} on ${on_string}: final evidence" /> - <data name="finalscaffolds" format="fasta" label="${tool.name} on ${on_string}: final scaffolds" /> - <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" /> - <data name="summaryfile" format="txt" label="${tool.name} on ${on_string}: summary" /> + <data name="finalevidence" format="txt" label="${tool.name} on ${on_string}: final evidence" from_work_dir="sspace.final.evidence" /> + <data name="finalscaffolds" format="fasta" label="${tool.name} on ${on_string}: final scaffolds" from_work_dir="sspace.final.scaffolds.fasta" /> + <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="sspace.logfile.txt" /> + <data name="summaryfile" format="txt" label="${tool.name} on ${on_string}: summary" from_work_dir="sspace.summaryfile.txt" /> </outputs> <tests>
--- a/tool_dependencies.xml Tue Sep 17 09:41:18 2013 -0400 +++ b/tool_dependencies.xml Fri Feb 21 04:17:55 2014 -0500 @@ -13,13 +13,10 @@ <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> </action> - <action type="set_environment"> - <environment_variable name="SSPACE_SITE_OPTIONS" action="set_to">"-T 1"</environment_variable> - </action> </actions> </install> <readme> -Change the SSPACE_SITE_OPTIONS variable in the installed env.sh file to adjust the number of threads to use in Bowtie alignment (-T). +Configuration: Previously (until Release 0), the SSPACE_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of threads to use in Bowtie alignment (-T). This is not used anymore and may be removed. </readme> </package> </tool_dependency>