Mercurial > repos > sanbi-uwc > build_ctb_gene
changeset 26:51a48982f643 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit a8d49944fccca430c0d79782f01e8e8758161cb8
| author | sanbi-uwc |
|---|---|
| date | Fri, 20 May 2016 06:25:15 -0400 |
| parents | 329bd8a876a6 |
| children | 3995dfb6b497 |
| files | build_ctb_gene.py build_ctb_gene.xml |
| diffstat | 2 files changed, 14 insertions(+), 5 deletions(-) [+] |
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--- a/build_ctb_gene.py Fri May 20 05:24:24 2016 -0400 +++ b/build_ctb_gene.py Fri May 20 06:25:15 2016 -0400 @@ -61,6 +61,9 @@ os.chdir(self.args.outputdir) shutil.copytree(file_name, file_name.rsplit('/', 1)[-1]) + def docker_boot(self): + cmd = 'docker run -d --name build_ctb_gene thoba/neo4j_galaxy_ie' + check_call(cmd) def main(): parser = argparse.ArgumentParser(description="Tool used to extract data about genes using locus_tags") @@ -74,6 +77,14 @@ parser.add_argument('--port') args = parser.parse_args() + ctb_gene_runner = BuildCtbRunner(args) + ctb_gene_runner.build_ctb_gene() + + # boot up a neo4j docker container + ctb_gene_runner.docker_boot() + + # docker_cmd = 'docker run ' + export_cmd = "export NEO4J_REST_URL=http://${args.username}:${args.password}@${args.url}:${args.port}/db/data/" try: os.system(export_cmd) @@ -84,8 +95,6 @@ if not os.path.exists(args.outputdir): os.makedirs(args.outputdir) - ctb_gene_runner = BuildCtbRunner(args) - ctb_gene_runner.build_ctb_gene() if __name__ == "__main__": main()
--- a/build_ctb_gene.xml Fri May 20 05:24:24 2016 -0400 +++ b/build_ctb_gene.xml Fri May 20 06:25:15 2016 -0400 @@ -13,13 +13,13 @@ </command> <inputs> <param name="input_file" type="data" format="gff" label="Choose the GFF file" help="Specify the GFF file" optional="False" /> - <param type="text" name="neo4j_data_mount_point" value="" label="Neo4j data mount point" place-holder="/mnt/neo4j/data/lib" optional="False" /> - <section name="db_settings" title="Neo4j Backend Database Settings" expanded="True"> + <!--<param type="text" name="neo4j_data_mount_point" value="" label="Neo4j data mount point" place-holder="/mnt/neo4j/data/lib" optional="False" /> --> + <!--<section name="db_settings" title="Neo4j Backend Database Settings" expanded="True"> <param type="text" name="neo4j_db_url" value="" label="Neo4j database URL" optional="False" /> <param type="text" name="neo4j_db_port" value="" label="Neo4j database port" optional="False" /> <param type="text" name="neo4j_db_username" value="" label="Neo4j database username" optional="False" /> <param type="text" name="neo4j_db_password" value="" label="Neo4j database password" optional="False" /> - </section> + </section>--> </inputs> <outputs> <data format="neostore" name="outputFile1"/>