changeset 0:f1f1f8437f7c draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/genetorrent/genetorrent.py	Fri Jun 14 18:19:17 2013 -0400
@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+
+import sys
+import subprocess
+import os
+import shutil
+from glob import glob
+import json
+
+def which(cmd):
+	cmd = ["which",cmd]
+	p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
+	res = p.stdout.readline().rstrip()
+	if len(res) == 0: return None
+	return res
+
+if __name__ == "__main__":
+	uuid = sys.argv[1]
+	cred_file = sys.argv[2]
+	output = sys.argv[3]
+	output_id = int(sys.argv[4])
+
+	gtdownload = which("gtdownload")
+	if gtdownload is None:
+		sys.stderr.write("gtdownload not found\n")
+		handle.close()
+		sys.exit(1)
+	
+	cred_dir = os.path.join(os.path.dirname(os.path.dirname(gtdownload)), "share", "GeneTorrent")
+	serr = open("std.error", "w")
+	
+	proc = subprocess.Popen( [gtdownload, "-c", cred_file, "-C", cred_dir, "-d", uuid, "-vv"], stderr=serr )
+	proc.communicate()
+	serr.close()	
+
+	copied = False
+	for f in glob(os.path.join(uuid, "*.bam")):
+		copied = True
+		shutil.move(f, output)
+	
+	if not copied:
+		handle = open("std.error")
+		sys.stderr.write(handle.read())
+		handle.close()
+		sys.exit(1)
+
+	json_file = open( 'galaxy.json', 'w' )
+	info = dict( type = 'dataset',
+				 ext = "bam",
+				 name = uuid + " CGHub BAM",
+				 uuid = uuid,
+				dataset_id = output_id 
+			)
+	json_file.write( json.dumps( info ) )
+	json_file.close()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/genetorrent/genetorrent.xml	Fri Jun 14 18:19:17 2013 -0400
@@ -0,0 +1,21 @@
+<tool id="cghub_genetorrent" name="CGHub GeneTorrent" version="1.0.0">
+	<description>download BAM files from CGHub</description>
+		<command interpreter="python">
+genetorrent.py $uuid $cred_file $outfile $outfile.dataset.dataset.id
+		</command>
+		<inputs>
+			<param name="uuid" type="text" size="50" label="Analysis ID"/>
+			<param name="cred_file" type="select" label="Download Credentials">
+				<options from_file="cghub_credentials.loc">
+					<column name="name" index="0"/>
+					<column name="value" index="1"/>
+				</options>
+			</param>
+		</inputs>
+		<outputs>
+			<data name="outfile" format="bam" label="${uuid} BAM"/>
+		</outputs>
+		<help>
+Download BAM files from CGHub
+		</help>
+</tool>