# HG changeset patch
# User sanbi-uwc
# Date 1463739915 14400
# Node ID 51a48982f643f2c161acf623aa69f4b9ecc79675
# Parent 329bd8a876a6787feba93e67cdfa1f73bcc46286
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit a8d49944fccca430c0d79782f01e8e8758161cb8
diff -r 329bd8a876a6 -r 51a48982f643 build_ctb_gene.py
--- 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()
diff -r 329bd8a876a6 -r 51a48982f643 build_ctb_gene.xml
--- 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 @@
-
-