Mercurial > repos > sanbi-uwc > data_manager_novoalign_index_builder
changeset 3:b63a406719c5 draft
planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 91d41d6ac8f81ef614491ed45e129d08b6471545
| author | sanbi-uwc |
|---|---|
| date | Fri, 04 Mar 2016 02:47:10 -0500 |
| parents | e51fb8188ed9 |
| children | 1b70cac31576 |
| files | data_manager/novoalign_index_builder.py tool-data/novocraft_index.nix.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 20 insertions(+), 10 deletions(-) [+] |
line wrap: on
line diff
--- a/data_manager/novoalign_index_builder.py Thu Mar 03 08:40:42 2016 -0500 +++ b/data_manager/novoalign_index_builder.py Fri Mar 04 02:47:10 2016 -0500 @@ -1,6 +1,7 @@ #!/usr/bin/env python # Z. Mashologu (SANBI-UWC) # import dict as dict +from __future__ import print_function import os import sys import urllib2 @@ -8,7 +9,6 @@ import argparse import shlex from subprocess import check_call, CalledProcessError -from __future__ import print_function log = logging.getLogger(__name__) @@ -41,11 +41,12 @@ else: nslots = 1 - cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadN {}'.format( - target_directory, - fasta_filename, - nslots) - cmdline = shlex.split(cmdline_str) + #cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadN {}'.format( + # target_directory, + # fasta_filename, + # nslots) + #cmdline = shlex.split(cmdline_str) + cmdline = ('touch', '{}/foo.nix'.format(target_directory)) try: check_call(cmdline) except CalledProcessError: @@ -72,22 +73,23 @@ def main(): parser = argparse.ArgumentParser(description="Generate Novo-align genome index and JSON describing this") parser.add_argument('output_filename') + parser.add_argument('--dbkey_description') parser.add_argument('--data_table_name', default='novocraft_index') - (options, args) = parser.parse_args() + args = parser.parse_args() filename = args.output_filename params = loads(open(filename).read()) target_directory = params['output_data'][0]['extra_files_path'] - os.mkdir(target_directory) + os.makedirs(target_directory) - dbkey, sequence_id, sequence_name = get_dbkey_id_name(params, dbkey_description=options.dbkey_description) + dbkey, sequence_id, sequence_name = get_dbkey_id_name(params, dbkey_description=args.dbkey_description) if dbkey in [None, '', '?']: raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey)) # Fetch the FASTA REFERENCE_SOURCE_TO_DOWNLOAD[params['param_dict']['reference_source']['reference_source_selector']]\ - (params, target_directory, dbkey, sequence_id, sequence_name) + (params, target_directory) data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=target_directory)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/novocraft_index.nix.sample Fri Mar 04 02:47:10 2016 -0500 @@ -0,0 +1,2 @@ +#TODO: Document +#<unique_build_id> <dbkey> <display_name> <directory_path>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Mar 04 02:47:10 2016 -0500 @@ -0,0 +1,6 @@ +<tables> + <table name="novocraft_index" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/novocraft_index.nix" /> + </table> +</tables>