| Previous changeset 1:a580422f6f1d (2014-08-26) Next changeset 3:172815da3d41 (2017-04-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_database_downloader commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4 |
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modified:
data_manager/data_manager_gemini_download.py data_manager/data_manager_gemini_download.xml tool_dependencies.xml |
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| diff -r a580422f6f1d -r 345412d58d75 data_manager/data_manager_gemini_download.py --- a/data_manager/data_manager_gemini_download.py Tue Aug 26 19:58:38 2014 -0400 +++ b/data_manager/data_manager_gemini_download.py Thu Feb 18 08:49:06 2016 -0500 |
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| @@ -10,19 +10,16 @@ def main(): today = datetime.date.today() - gemini_root_dir = os.environ['GEMINI_ROOT_DIR'] params = json.loads( open( sys.argv[1] ).read() ) target_directory = params[ 'output_data' ][0]['extra_files_path'] os.mkdir( target_directory ) - gemini_exec = os.path.join( gemini_root_dir, 'gemini', 'gemini', 'install-data.py' ) - cmd = gemini_exec + " %s %s" % (' '.join( [params['param_dict']['gerp_bp'], params['param_dict']['cadd']] ), target_directory) - #cmd = gemini_exec + " --help > %s/foo.txt" % target_directory + cmd = "gemini --annotation-dir %s update --dataonly %s %s" % (target_directory, params['param_dict']['gerp_bp'], params['param_dict']['cadd'] ) ret = subprocess.check_call( cmd, shell=True ) - data_manager_dict = { - 'data_tables': - {'gemini_databases': [ - {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() } - ] + data_manager_dict = { + 'data_tables': + {'gemini_databases': [ + {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() } + ] } } |
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| diff -r a580422f6f1d -r 345412d58d75 data_manager/data_manager_gemini_download.xml --- a/data_manager/data_manager_gemini_download.xml Tue Aug 26 19:58:38 2014 -0400 +++ b/data_manager/data_manager_gemini_download.xml Thu Feb 18 08:49:06 2016 -0500 |
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| @@ -1,32 +1,31 @@ -<tool id="data_manager_gemini_download" name="GEMINI Download" version="0.10.0" tool_type="manage_data"> +<tool id="data_manager_gemini_download" name="GEMINI Download" version="0.18.1" tool_type="manage_data"> <description>Download a new database</description> <requirements> - <requirement type="package" version="0.10.0">gemini</requirement> + <requirement type="package" version="0.18.1">gemini</requirement> </requirements> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> <command interpreter="python"> data_manager_gemini_download.py "$out_file" </command> <inputs> - <param name="cadd" type="boolean" truevalue="--extra cadd_score" falsevalue="" checked="True" + <param name="cadd" type="boolean" truevalue="--extra cadd_score" falsevalue="" checked="True" label="Download CADD scores for GEMINI database annotation" help="(--extra cadd_score)"/> - - <param name="gerp_bp" type="boolean" truevalue="--extra gerp_bp" falsevalue="" checked="True" + <param name="gerp_bp" type="boolean" truevalue="--extra gerp_bp" falsevalue="" checked="True" label="Download GERP for GEMINI database annotation" help="(--extra gerp_bp)"/> </inputs> <outputs> <data name="out_file" format="data_manager_json" label="${tool.name}"/> </outputs> - <stdio> - <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> <tests> </tests> <help> This tool downloads the GEMINI databases. -For details about this tool, please go to http://http://gemini.readthedocs.org +For details about this tool, please go to http://gemini.readthedocs.org </help> <citations> |
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| diff -r a580422f6f1d -r 345412d58d75 tool_dependencies.xml --- a/tool_dependencies.xml Tue Aug 26 19:58:38 2014 -0400 +++ b/tool_dependencies.xml Thu Feb 18 08:49:06 2016 -0500 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="gemini" version="0.10.0"> - <repository changeset_revision="42c72725f879" name="package_gemini_0_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="gemini" version="0.18.1"> + <repository changeset_revision="be869e11582f" name="package_gemini_0_18_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |