Mercurial > repos > iuc > data_manager_gemini_database_downloader
changeset 2:ffa94ffe1179 draft
Uploaded
| author | iuc |
|---|---|
| date | Sun, 17 Aug 2014 08:05:04 -0400 |
| parents | 50405cb4f8cd |
| children | 7cfa2506531d |
| files | data_manager/data_manager_gemini_download.py data_manager/data_manager_gemini_download.xml data_manager_conf.xml tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 5 files changed, 10 insertions(+), 5 deletions(-) [+] |
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--- a/data_manager/data_manager_gemini_download.py Sat Aug 16 12:33:49 2014 -0400 +++ b/data_manager/data_manager_gemini_download.py Sun Aug 17 08:05:04 2014 -0400 @@ -6,11 +6,17 @@ def main(): + + print sys.argv[1] params = json.loads( open( sys.argv[1] ).read() ) + print 'KKKKKKKKKKKKKK',params target_directory = params[ 'output_data' ][0]['extra_files_path'] os.mkdir( target_directory ) data_manager_dict = { 'data_tables': {'gemini_databases': [ {'value': sys.argv[2], 'name': sys.argv[3], 'path': target_directory }] } } + with open(os.path.join(target_directory, 'help.txt'), 'w+') as h: + h.write('##############') + #save info to json file with open( sys.argv[1], 'wb' ) as out: out.write( json.dumps( data_manager_dict ) )
--- a/data_manager/data_manager_gemini_download.xml Sat Aug 16 12:33:49 2014 -0400 +++ b/data_manager/data_manager_gemini_download.xml Sun Aug 17 08:05:04 2014 -0400 @@ -4,7 +4,6 @@ <requirement type="package" version="0.9.1">gemini</requirement> </requirements> <command interpreter="python"> - #from galaxy.util.json import from_json_string, to_json_string ##\$GEMINI_ROOT_DIR/gemini/gemini/install-data.py /home/bag/test/gdata/ $gerp_bp $cadd_score data_manager_gemini_download.py "$out_file" "foo" "bar"
--- a/data_manager_conf.xml Sat Aug 16 12:33:49 2014 -0400 +++ b/data_manager_conf.xml Sun Aug 17 08:05:04 2014 -0400 @@ -7,9 +7,9 @@ <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="${GALAXY_DATA_MANAGER_DATA_PATH}">gemini/data</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">gemini/data/${value}/${path}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gemini/data</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gemini/data/${value}/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>
--- a/tool_data_table_conf.xml.sample Sat Aug 16 12:33:49 2014 -0400 +++ b/tool_data_table_conf.xml.sample Sun Aug 17 08:05:04 2014 -0400 @@ -1,6 +1,6 @@ <tables> <table name="gemini_databases" comment_char="#"> - <columns>value, name</columns> + <columns>value, name, path</columns> <file path="tool-data/gemini_databases.loc" /> </table> </tables>
--- a/tool_dependencies.xml Sat Aug 16 12:33:49 2014 -0400 +++ b/tool_dependencies.xml Sun Aug 17 08:05:04 2014 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="gemini" version="0.9.1"> - <repository changeset_revision="610ebefc0db1" name="package_gemini_0_9_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a10ebb5a71bb" name="package_gemini_0_9_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>