Mercurial > repos > iuc > data_manager_gemini_database_downloader
changeset 0:fd9e9ac5ecb3 draft
Imported from capsule None
| author | iuc |
|---|---|
| date | Mon, 25 Aug 2014 17:15:46 -0400 |
| parents | |
| children | a580422f6f1d |
| files | data_manager/data_manager_gemini_download.py data_manager/data_manager_gemini_download.xml data_manager_conf.xml tool-data/gemini_databases.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 6 files changed, 109 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_gemini_download.py Mon Aug 25 17:15:46 2014 -0400 @@ -0,0 +1,35 @@ +#!/usr/bin/env python + +import sys +import os +import json +import shlex +import datetime +import subprocess + +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 + 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() } + ] + } + } + + #save info to json file + with open( sys.argv[1], 'wb' ) as out: + out.write( json.dumps( data_manager_dict ) ) + +if __name__ == "__main__": + main() +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_gemini_download.xml Mon Aug 25 17:15:46 2014 -0400 @@ -0,0 +1,37 @@ +<tool id="data_manager_gemini_download" name="GEMINI Download" version="0.9.1" tool_type="manage_data"> + <description>Download a new database</description> + <requirements> + <requirement type="package" version="0.10.0">gemini</requirement> + </requirements> + <command interpreter="python"> + data_manager_gemini_download.py "$out_file" + </command> + <inputs> + <param name="cadd" type="boolean" truevalue="--extra cadd_score" falsevalue="" checked="True" + label="Download CADD scores for GEMINI database annotation" help="(--extra cadd_score)"/> + + <param name="gerp_bp" type="boolean" truevalue="--extra gerp_bp" falsevalue="" checked="True" + label="Download GERP for GEMINI database annotation" help="(--extra gerp_bp)"/> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" label="${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 + + </help> + <citations> + <citation type="doi">10.1371/journal.pcbi.1003153</citation> + <yield /> + </citations> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Mon Aug 25 17:15:46 2014 -0400 @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_gemini_download.xml" id="data_manager_gemini_download" > + <data_table name="gemini_databases"> <!-- Defines a Data Table to be modified. --> + <output> <!-- Handle the output of the Data Manager Tool --> + <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="dbkey" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="path" output_ref="out_file" > + <move type="directory" relativize_symlinks="True"> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">gemini/data/${dbkey}/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gemini/data/${dbkey}/${value}/gemini/data/</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers> + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/gemini_databases.loc.sample Mon Aug 25 17:15:46 2014 -0400 @@ -0,0 +1,3 @@ +## GEMINI databases +#Version dbkey Description +#08_08_2014 hg19 Database (08-08-2014)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Aug 25 17:15:46 2014 -0400 @@ -0,0 +1,7 @@ +<tables> + <table name="gemini_databases" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/gemini_databases.loc" /> + </table> +</tables> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Aug 25 17:15:46 2014 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="gemini" version="0.10.0"> + <repository name="package_gemini_0_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>