# HG changeset patch
# User jeremyjliu
# Date 1421026809 18000
# Node ID 8bf194e522bfd00391eeae3dc4bc300990b60c5f
# Parent  d5faf2b51b07c47960eeaad9207e2b22d69c9576
Uploaded

diff -r d5faf2b51b07 -r 8bf194e522bf data_manager/test.py
--- a/data_manager/test.py	Sun Jan 11 20:30:46 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-#!/usr/bin/env python
-import optparse
-
-def main():
-    #Parse Command Line
-    parser = optparse.OptionParser()
-    parser.add_option( '-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description' )
-    (options, args) = parser.parse_args()
-    
-    filename = args[0]
-    print(args)
-
-main()
\ No newline at end of file
diff -r d5faf2b51b07 -r 8bf194e522bf tool-data/all_fasta.loc.sample
--- a/tool-data/all_fasta.loc.sample	Sun Jan 11 20:30:46 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-#This file lists the locations and dbkeys of all the fasta files
-#under the "genome" directory (a directory that contains a directory
-#for each build). The script extract_fasta.py will generate the file
-#all_fasta.loc. This file has the format (white space characters are
-#TAB characters):
-#
-#<unique_build_id>	<dbkey>		<display_name>	<file_path>
-#
-#So, all_fasta.loc could look something like this:
-#
-#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3/apiMel3.fa
-#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
-#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
-#
-#Your all_fasta.loc file should contain an entry for each individual
-#fasta file. So there will be multiple fasta files for each build,
-#such as with hg19 above.
-#
diff -r d5faf2b51b07 -r 8bf194e522bf tool-data/motif_databases.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/motif_databases.loc.sample	Sun Jan 11 20:40:09 2015 -0500
@@ -0,0 +1,9 @@
+#
+#<value>		<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#test	  Test Pouya Subset (hg19)		  /<path_to_galaxy>/tool-data/motifs/pouya_test_motifs.bed.bgz
+#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
+#