Mercurial > repos > melissacline > xena_import
diff xena_import.py @ 3:cae2b765ca5d
Changing how the Xena base dir is communicated
| author | melissacline |
|---|---|
| date | Wed, 03 Sep 2014 16:02:24 -0700 |
| parents | b3cd322f7749 |
| children | 8d87f0ecc08d |
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--- 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)