Mercurial > repos > greg > plant_tribes_gene_family_aligner
view run_pasta.py @ 11:1c5a484fc06f draft default tip
planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/gene_family_aligner commit f7690d10e0515911ee00455806e457bc53f145c7-dirty
author | greg |
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date | Thu, 13 Jun 2024 11:54:31 +0000 |
parents | 7ba9469800b9 |
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#! /usr/bin/env python """Main script of PASTA in command-line mode - this simply invokes the main function found in pasta/mainpasta.py """ # This file is part of PASTA which is forked from SATe # PASTA like SATe is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program 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 General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. # Jiaye Yu and Mark Holder, University of Kansas if __name__ == "__main__": import os import sys from pasta.mainpasta import pasta_main from pasta import MESSENGER sys.setrecursionlimit(100000) _PASTA_DEBUG = os.environ.get('PASTA_DEBUG') _DEVELOPER = _PASTA_DEBUG and _PASTA_DEBUG != '0' if not _DEVELOPER: _PASTA_DEVELOPER = os.environ.get('PASTA_DEVELOPER') _DEVELOPER = _PASTA_DEVELOPER and _PASTA_DEVELOPER != '0' try: rc, temp_dir, temp_fs = pasta_main() if not rc: raise ValueError("Unknown PASTA execution error") if (temp_dir is not None) and (os.path.exists(temp_dir)): MESSENGER.send_info("Note that temporary files from the run have not been deleted, they can be found in:\n '%s'\n" % temp_dir) if sys.platform.lower().startswith('darwin') and ("'" not in temp_dir): MESSENGER.send_info(''' If you cannot see this directory in the Finder application, you may want to use the 'open' command executed from a Terminal. You can do this by launching the /Applications/Utilities/Terminal program and then typing open '%s' followed by a return at the prompt. If the argument to the open command is a directory, then it should open a Finder window in the directory (even if that directory is hidden by default). ''' % temp_dir) except Exception as x: if _DEVELOPER: raise message = "PASTA is exiting because of an error:\n%s " % str(x) try: from pasta import MESSENGER MESSENGER.send_error(message) except: sys.stderr.write(message) sys.exit(1)