# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1413211179 18000
# Node ID 532a336a14c1329c7dd8d766c1fcf960c2d27c5a
# Parent  fbbbc9fd8fb9ff719f8e682614d134991d9f3113
Need all_fasta.loc for cummerbund

diff -r fbbbc9fd8fb9 -r 532a336a14c1 tool-data/all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Mon Oct 13 09:39:39 2014 -0500
@@ -0,0 +1,18 @@
+#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 fbbbc9fd8fb9 -r 532a336a14c1 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Mon Oct 13 09:29:20 2014 -0500
+++ b/tool_data_table_conf.xml.sample	Mon Oct 13 09:39:39 2014 -0500
@@ -1,4 +1,9 @@
 <tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
     <table name="fasta_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/fasta_indexes.loc" />