# HG changeset patch
# User melissacline
# Date 1409772885 14400
# Node ID b3cd322f77490b789b83965ad1715d97faeb3617
# Parent a42384446daf3bc9d7f4ed7f4f4db586b907d64c
Uploaded
diff -r a42384446daf -r b3cd322f7749 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Sep 03 15:34:45 2014 -0400
@@ -0,0 +1,12 @@
+
+
+
+
+
+
+ $INSTALL_DIR/xena
+
+
+
+
+
diff -r a42384446daf -r b3cd322f7749 xena_import.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/xena_import.py Wed Sep 03 15:34:45 2014 -0400
@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+
+"""
+ xena_import.py: import a dataset into Xena
+
+ Given a cmdline-specified genomic data file and a cmdline-specified Xena
+ directory, import the genomic data fle into Xena. This requires assembling
+ the necessary json file, based on cmdline input.
+"""
+
+import argparse
+import json
+import shutil
+
+def main():
+ parser = argparse.ArgumentParser()
+ 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()
+
+ # Assemble the metadata in JSON format
+ metadata = { 'cohort': args.cohort, 'type': args.type }
+ jsonMetadata = json.dumps(metadata, indent=2)
+
+ # Write the metadata to a file in the Xena directory. Use the filename
+ # of the genomic data file, with an added .json extension.
+ genomicDataFilename = args.genomicDataPathname.split("/")[-1]
+ jsonMetadataPathname = "%s/%s.json" % (args.xenaInputDir,
+ genomicDataFilename)
+ fp = open(jsonMetadataPathname, "w")
+ fp.write("%s\n" % (jsonMetadata))
+ fp.close()
+
+ # Finally, copy the genomic data into the Xena directory
+ shutil.copy(args.genomicDataPathname, args.xenaInputDir)
+
+if __name__ == "__main__":
+ main()
diff -r a42384446daf -r b3cd322f7749 xena_import.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/xena_import.xml Wed Sep 03 15:34:45 2014 -0400
@@ -0,0 +1,17 @@
+
+ Import into the Xena VM
+
+ installXena2
+
+
+ xena_import.py ${xenaInputData} ${cohort} ${metadataType} ${XENA_BASE_DIR}/files/
+
+
+
+
+
+
+
+ To Appear
+
+