Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 1:32d04371ed19 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
| author | dfornika |
|---|---|
| date | Thu, 28 Feb 2019 13:59:33 -0500 |
| parents | 7e43f66abe9d |
| children | cf0cda80b659 |
| files | data_manager/kraken2_build_standard.py tool-data/kraken2_databases.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 2 files changed, 19 insertions(+), 2 deletions(-) [+] |
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--- a/data_manager/kraken2_build_standard.py Thu Feb 28 02:32:38 2019 -0500 +++ b/data_manager/kraken2_build_standard.py Thu Feb 28 13:59:33 2019 -0500 @@ -27,13 +27,22 @@ '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), '--db', database_name ] - pprint(args) proc = subprocess.Popen(args=args, shell=False, cwd=target_directory) return_code = proc.wait() if return_code: print("Error building database.", file=sys.stderr) sys.exit( return_code ) - + args = [ + 'kraken2-build', + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', database_name + ] + proc = subprocess.Popen(args=args, shell=False, cwd=target_directory) + return_code = proc.wait() + if return_code: + print("Error building database.", file=sys.stderr) + sys.exit( return_code ) data_table_entry = { "value": database_name, "name": database_name,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Feb 28 13:59:33 2019 -0500 @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of Kraken database in the required format --> + <table name="kraken2_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/kraken2_databases.loc" /> + </table> +</tables>