# HG changeset patch # User sanbi-uwc # Date 1463386819 14400 # Node ID 714cbeae0b96955379b8ee102387181d0a3dda43 # Parent 65558b5914fcebb265a263146a78f68e1a0f0c20 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535 diff -r 65558b5914fc -r 714cbeae0b96 build_ctb_gene.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build_ctb_gene.py Mon May 16 04:20:19 2016 -0400 @@ -0,0 +1,61 @@ +#!/usr/bin/env python +from __future__ import print_function +import argparse +import os +import sys +import glob + +import logging +log = logging.getLogger( __name__ ) + +def build_ctb_gene(output_file1, output_dir, input_file, mount_point ): + #cmdline_str = "build_ctb_gene goterms ${}".format(input_file) + cmdline_str = "echo goterms" + build_ctb = False + try: + os.system(cmdline_str) + build_ctb = True + except: + log.debug("Error running the build_ctb_gene goterms", file=sys.stderr) + + # Read the files at the mount point and load the html file + if build_ctb == True: + files=glob.glob(mount_point) + output_file1 = """ + + + + + + + +
+ + + """ + for file in files: + output_file1 += """""" + output_file1 += """
Files
file
\n""" + + +def main(): + parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool") + parser.add_argument('output_file1') + parser.add_argument('output_dir') + parser.add_argument('--input_file') + parser.add_argument('--mount_point') + parser.add_argument('--username') + parser.add_argument('--password') + parser.add_argument('--url') + parser.add_argument('--port') + args = parser.parse_args() + + export_cmd = "export NEO4J_REST_URL=http://${neo4j_db_username}:${neo4j_db_password}@${neo4j_db_url}:${neo4j_db_port}/db/data/" + try: + os.system(export_cmd) + except: + log.debug("Error exporting the NEO4J db environmental values") + + build_ctb_gene(args.output_file1, args.output_dir, args.input_file, args.mount_point) + +if __name__ == "__main__": main() diff -r 65558b5914fc -r 714cbeae0b96 build_ctb_gene.xml --- a/build_ctb_gene.xml Tue May 10 14:55:23 2016 -0400 +++ b/build_ctb_gene.xml Mon May 16 04:20:19 2016 -0400 @@ -1,26 +1,63 @@ - build_ctb_gene + build_ctb_gene_neo4j build_ctb_gene is the tool used to extract data about genes using locus_tags - - export NEO4J_REST_URL=http://${neo4j_db_username}:${neo4j_db_password}@${neo4j_db_url}:${neo4j_db_port}/db/data/ && - build_ctb_gene goterms ${input_file} + + build_ctb_gene.py '${outputFile1}' --outputdir ${outputFile2.files_path} --input_file ${input_file} --mount_point ${neo4j_data_mount_point} \ + --username ${neo4j_db_username} --password ${neo4j_db_password} --url ${neo4j_db_url} --port ${neo4j_db_port} - - - - + +
+ + + + +
- + + + Help!