Mercurial > repos > crs4 > mugsy
changeset 0:1e8862eb2eba draft
Uploaded
| author | crs4 |
|---|---|
| date | Fri, 06 Sep 2013 05:58:59 -0400 |
| parents | |
| children | 2dcf5873f1b1 |
| files | COPYING mugsy.py mugsy.xml tool_dependencies.xml |
| diffstat | 4 files changed, 167 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Fri Sep 06 05:58:59 2013 -0400 @@ -0,0 +1,23 @@ +Copyright © 2012-2013 CRS4 Srl. http://www.crs4.it/ +Created by: +Massimiliano Orsini <massimiliano.orsini@crs4.it> +Nicola Soranzo <nicola.soranzo@crs4.it> + +Permission is hereby granted, free of charge, to any person obtaining a +copy of this software and associated documentation files (the +"Software"), to deal in the Software without restriction, including +without limitation the rights to use, copy, modify, merge, publish, +distribute, sublicense, and/or sell copies of the Software, and to +permit persons to whom the Software is furnished to do so, subject to +the following conditions: + +The above copyright notice and this permission notice shall be included +in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. +IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY +CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, +TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE +SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mugsy.py Fri Sep 06 05:58:59 2013 -0400 @@ -0,0 +1,48 @@ +# -*- coding: utf-8 -*- +""" +Mugsy wrapper + +For draft genomes a single multi-FASTA file containig all contigs should be provided. +""" + +import optparse +import os +import shutil +import subprocess +import sys +import tempfile + +def __main__(): + """ main function """ + parser = optparse.OptionParser() + parser.add_option('-r', dest='reference', help='reference FASTA file') + parser.add_option('-c', dest='contigs', help='contigs FASTA file') + parser.add_option('-p', dest='prefix', default='prefix', help='prefix ') + parser.add_option('-l', dest='logfile', help='logfile') + parser.add_option('--ml', dest='mugsylog', help='mugsylog file') + parser.add_option('--maf', dest='maf', help='ouput MAF alignment file ') + (options, args) = parser.parse_args() + if len(args) > 0: + parser.error('Wrong number of arguments') + + logfile = options.logfile + wd = tempfile.mkdtemp() + try: + command = "mugsy --directory %s --prefix %s --log %s %s %s" % (wd, options.prefix, options.mugsylog, options.reference, options.contigs) + print 'Mugsy command to be executed:\n ' + command + + log = open(logfile, 'w') if logfile else sys.stdout + try: + subprocess.check_call(command, stderr=log, shell=True) # need to redirect stderr because mugsy writes its logging info there + finally: + if log != sys.stdout: + log.close() + print 'Mugsy executed!' + + shutil.move(os.path.join(wd, options.prefix + '.maf'), options.maf) + finally: + shutil.rmtree(wd) + + +if __name__ == "__main__": + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mugsy.xml Fri Sep 06 05:58:59 2013 -0400 @@ -0,0 +1,44 @@ +<tool id="mugsy" name="Mugsy" version="1.0.1"> + <description>multiple whole genome aligner</description> + <requirements> + <requirement type="package" version="1.2.3.1">mugsy</requirement> + </requirements> + <command interpreter="python"> + mugsy.py -r $reference -c $contigs -l $logfile --ml $mugsylog --maf $maffile + </command> + + <inputs> + <param name="reference" type="data" format="fasta" label="Reference" help="FASTA format" /> + <param name="contigs" type="data" format="fasta" label="Contigs/draft" help="FASTA format" /> + </inputs> + <outputs> + <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" /> + <data name="mugsylog" format="txt" label="${tool.name} on ${on_string}: mugsy.log" /> + <data name="maffile" format="maf" label="${tool.name} on ${on_string}: MAF" /> + </outputs> + <tests> + + </tests> + <help> +**What it does** + +Mugsy generates a MAF (multiple alignment format) file containing the multiple alignments from FASTA inputs. + +This implementation runs with two files only: reference vs contigs/draft(s). For multiple alignment a single Multi-FASTA file containing all contigs should be provided. + +**License and citation** + +This Galaxy tool is Copyright © 2012-2013 `CRS4 Srl.`_ and is released under the `MIT license`_. + +.. _CRS4 Srl.: http://www.crs4.it/ +.. _MIT license: http://opensource.org/licenses/MIT + +If you use this tool in Galaxy, please cite the website http://orione.crs4.it/ + +This tool uses `Mugsy`_, which is licensed separately. Please cite |Angiuoli2010|_. + +.. _Mugsy: http://mugsy.sourceforge.net/ +.. |Angiuoli2010| replace:: Angiuoli, S. V., Salzberg S. L. (2010) Mugsy: Fast multiple alignment of closely related whole genomes. *Bioinformatics* 27(3), 334-342 +.. _Angiuoli2010: http://bioinformatics.oxfordjournals.org/content/27/3/334 + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Sep 06 05:58:59 2013 -0400 @@ -0,0 +1,52 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="boost" version="1.53.0"> + <repository changeset_revision="dbdde1a2d0c5" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="mugsy" version="1.2.3.1"> + <install version="1.0"> + <actions> + <!-- checkout from svn source repository into a directory with the same name of the package, which will be automatically used as working directory --> + <action type="shell_command">svn checkout http://svn.code.sf.net/p/mugsy/code/ mugsy</action> + <!-- fix for Boost >= 1.42.0 --> + <action type="shell_command">sed -i 's/boost\/property_map\.hpp/boost\/property_map\/property_map.hpp/' trunk/chaining/synchain-mugsy.cpp</action> + <!-- fix for Boost >= 1.47.0 --> + <action type="shell_command">sed -i 's/boost\/graph\/kolmogorov_max_flow\.hpp/boost\/graph\/boykov_kolmogorov_max_flow.hpp/' trunk/chaining/synchain-mugsy.cpp trunk/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp</action> + <!-- fix chaining Makefile --> + <action type="shell_command">sed -i -e 's/-static//g' -e 's/-lbgl-viz -lboost_graph-gcc41-mt//g' trunk/chaining/Makefile</action> + <!-- fix missing include in show-diff.cc --> + <action type="shell_command">sed -i '13 a \#include <algorithm>' trunk/MUMmer3.20/src/tigr/show-diff.cc</action> + <!-- skip make of streeproto.h since it would fail because of missing skproto.x --> + <action type="shell_command">touch trunk/MUMmer3.20/src/kurtz/streesrc/streeproto.h</action> + <!-- fix Makefile --> + <action type="shell_command">sed -i -e 's/install synchain-mugsy/install chaining\/synchain-mugsy/' -e 's/install mugsyWGA \(.*\)/install mugsy-seqan\/projects\/library\/apps\/mugsy\/gcc\/mugsy \1\/mugsyWGA/' trunk/Makefile</action> + <!-- fix MUMmer3.20 Makefile --> + <action type="shell_command">sed -i '/DOC_DIR/d' trunk/MUMmer3.20/Makefile</action> + <!-- populate the environment variables from the dependent repos --> + <action type="set_environment_for_install"> + <repository name="package_boost_1_53" owner="bgruening" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="boost" version="1.53.0" /> + </repository> + </action> + <!-- use $BOOST_ROOT_DIR in chaining Makefile --> + <action type="shell_command">sed -i -e 's/-I \/usr\/local\/projects\/angiuoli\/boost\/include\/boost-1_38/-I $(BOOST_ROOT_DIR)\/include/g' -e 's/-L \/usr\/local\/projects\/angiuoli\/boost\/lib\//-L $(BOOST_ROOT_DIR)\/lib/g' trunk/chaining/Makefile trunk/mugsy-seqan/platforms/gcc/platform.mak</action> + <!-- equivalent of make clean --> + <action type="shell_command">rm -f trunk/chaining/synchain-mugsy trunk/mugsyWGA trunk/synchain-mugsy && make -C trunk/MUMmer3.20 clean</action> + <action type="shell_command">make -C trunk all</action> + <action type="shell_command">make -C trunk install</action> + <action type="move_directory_files"> + <source_directory>trunk/mugsy_x86-64-v1r2.3.1</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> + </action> + <action type="set_environment"> + <environment_variable action="set_to" name="MUGSY_INSTALL">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + </readme> + </package> +</tool_dependency>