Mercurial > repos > sanbi-uwc > build_ctb_gene
diff build_ctb_gene.py @ 4:714cbeae0b96 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
| author | sanbi-uwc |
|---|---|
| date | Mon, 16 May 2016 04:20:19 -0400 |
| parents | |
| children | 6098213127d7 |
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--- /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 ${}".format(input_file) + cmdline_str = "echo goterms" + build_ctb = False + try: + os.system(cmdline_str) + build_ctb = True + except: + log.debug("Error running the build_ctb_gene goterms", file=sys.stderr) + + # Read the files at the mount point and load the html file + if build_ctb == True: + files=glob.glob(mount_point) + output_file1 = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> + <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> + <title></title> + <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> + </head> + <body> + <div class="toolFormBody"> + <table> + <th>Files</th> + """ + for file in files: + output_file1 += """<tr><td>file</td></tr>""" + output_file1 += """</table></div></body></html>\n""" + + +def main(): + parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool") + parser.add_argument('output_file1') + parser.add_argument('output_dir') + parser.add_argument('--input_file') + parser.add_argument('--mount_point') + parser.add_argument('--username') + parser.add_argument('--password') + parser.add_argument('--url') + parser.add_argument('--port') + args = parser.parse_args() + + export_cmd = "export NEO4J_REST_URL=http://${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()