# HG changeset patch
# User yhoogstrate
# Date 1392974545 18000
# Node ID ef69840982040a69f86056e172924a914acf1e99
# Parent  bdd5f2ecd087c25afce6826c0fce58b4c33ea94f
Uploaded

diff -r bdd5f2ecd087 -r ef6984098204 gene_sets.loc.sample
--- a/gene_sets.loc.sample	Mon Feb 17 10:49:18 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-# Because of this file, galaxy tools can access gene annotations
-# provided as GFF / GTF files by selecting on:
-# - Priorty (order in the file)
-# - Provider
-# - dbkey (reference genome id)
-# 
-# The gene_sets.loc file syntax is:
-# <name/UID> <dbkey> <path> <provider> <URL/reference*>
-#
-# *optional
-# 
-# In case you have TWO or MORE providers PER dbkey, the one mentioned
-# first in the file, should have the "default" priority.
-#
-
-
-
-# [UCSC - UCSC Genes: knownGene]
-
-#hg19.UCSC knownGene (mm/'yy)	hg19	/depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf	ucsc	http://genome.ucsc.edu/
-#hg18.UCSC knownGene (mm/'yy)	hg18	/depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf	ucsc	http://genome.ucsc.edu/
-
-
-
-# [RefSeq Genes: RefGene]
-# link: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/
-
-
-
-# [ Ensembl]
-# link: http://www.ensembl.org/info/data/ftp/index.html
-
-#Homo_sapiens.GRCh37.74	hg19	/depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf	ensembl	ftp://ftp.ensembl.org/pub/release-74/gtf/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gz
-#Homo_sapiens.NCBI36.54	hg18	/depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf	ensembl	ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz
diff -r bdd5f2ecd087 -r ef6984098204 tool-data/gene_sets.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gene_sets.loc.sample	Fri Feb 21 04:22:25 2014 -0500
@@ -0,0 +1,36 @@
+# Because of this file, galaxy tools can access gene annotations
+# provided as GFF / GTF files by selecting on:
+# - Priorty (order in the file)
+# - Provider
+# - dbkey (reference genome id)
+# 
+# The gene_sets.loc file syntax is:
+# <name/UID> <dbkey> <path> <provider> <URL/reference*>
+#
+# *optional
+# 
+# Please ensure maximally one TAB per column!
+# 
+# In case you have TWO or MORE providers PER dbkey, the one mentioned
+# first in the file, should have the "default" priority.
+#
+
+
+
+# [UCSC - UCSC Genes: knownGene]
+
+#hg19.UCSC knownGene (mm/'yy)	hg19	/depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf	ucsc	http://genome.ucsc.edu/
+#hg18.UCSC knownGene (mm/'yy)	hg18	/depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf	ucsc	http://genome.ucsc.edu/
+
+
+
+# [RefSeq Genes: RefGene]
+# link: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/
+
+
+
+# [ Ensembl]
+# link: http://www.ensembl.org/info/data/ftp/index.html
+
+#Homo_sapiens.GRCh37.74	hg19	/depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf	ensembl	ftp://ftp.ensembl.org/pub/release-74/gtf/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gz
+#Homo_sapiens.NCBI36.54	hg18	/depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf	ensembl	ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz
diff -r bdd5f2ecd087 -r ef6984098204 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Feb 21 04:22:25 2014 -0500
@@ -0,0 +1,5 @@
+<?xml version="1.0"?>
+<table name="gene_sets" comment_char="#">
+	<columns>name, dbkey, value, provider, reference</columns>
+	<file path="tool-data/gene_sets.loc.sample" /> 
+</table>
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