Mercurial > repos > melissacline > xena_import
changeset 3:cae2b765ca5d
Changing how the Xena base dir is communicated
| author | melissacline |
|---|---|
| date | Wed, 03 Sep 2014 16:02:24 -0700 |
| parents | b3cd322f7749 |
| children | 261a3d45a38a |
| files | tool_dependencies.xml xena_import.py xena_import.xml |
| diffstat | 3 files changed, 5 insertions(+), 3 deletions(-) [+] |
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--- a/tool_dependencies.xml Wed Sep 03 15:34:45 2014 -0400 +++ b/tool_dependencies.xml Wed Sep 03 16:02:24 2014 -0700 @@ -4,7 +4,8 @@ <install version="1.0"> <actions> <action type="set_environment"> - <environment_variable name="XENA_BASE_DIR" action="set_to">$INSTALL_DIR/xena</environment_variable> + <environment_variable name="XENA_BASE_DIR" action="set_to">${__tool_d\ +ata_path__}/shared//xena</environment_variable> </action> </actions> </install>
--- a/xena_import.py Wed Sep 03 15:34:45 2014 -0400 +++ b/xena_import.py Wed Sep 03 16:02:24 2014 -0700 @@ -17,9 +17,10 @@ parser.add_argument("genomicDataPathname", type=str) parser.add_argument("cohort", type=str) parser.add_argument("type", type=str) - parser.add_argument("xenaInputDir", type=str) args = parser.parse_args() + xenaBaseDir = os.getenv("XENA_BASE_DIR", "~") + # Assemble the metadata in JSON format metadata = { 'cohort': args.cohort, 'type': args.type } jsonMetadata = json.dumps(metadata, indent=2)
--- a/xena_import.xml Wed Sep 03 15:34:45 2014 -0400 +++ b/xena_import.xml Wed Sep 03 16:02:24 2014 -0700 @@ -4,7 +4,7 @@ <requirement type="package" version="1.0">installXena2</requirement> </requirements> <command interpreter="python"> - xena_import.py ${xenaInputData} ${cohort} ${metadataType} ${XENA_BASE_DIR}/files/ + xena_import.py ${xenaInputData} ${cohort} ${metadataType} </command> <inputs> <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/>