# HG changeset patch
# User cschu
# Date 1466974416 14400
# Node ID 5ef1c072f07cdf5b100a8ade44dbe6e0c29e3678
Uploaded
diff -r 000000000000 -r 5ef1c072f07c gffdm/.shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gffdm/.shed.yml Sun Jun 26 16:53:36 2016 -0400
@@ -0,0 +1,12 @@
+categories:
+- Data Managers
+- Metagenomics
+description: Contains a data manager that defines and populates the kraken_databases
+ tool data table.
+homepage_url:
+long_description: |
+ blah
+name: data_manager_load_featurecounts_gxf
+owner: cschu
+remote_repository_url:
+type: unrestricted
diff -r 000000000000 -r 5ef1c072f07c gffdm/data_manager/featurecounts_gxfloader.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gffdm/data_manager/featurecounts_gxfloader.xml Sun Jun 26 16:53:36 2016 -0400
@@ -0,0 +1,28 @@
+
+
+ GFF/GTF loader
+
+ featurecounts
+ FCOUNT_SCRIPT_PATH
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 5ef1c072f07c gffdm/data_manager/make_json.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gffdm/data_manager/make_json.py Sun Jun 26 16:53:36 2016 -0400
@@ -0,0 +1,33 @@
+import json
+import argparse
+import os
+import shutil
+
+
+
+parser = argparse.ArgumentParser(description='Create data manager json.')
+parser.add_argument('--dbkey', action='store')
+parser.add_argument('--provider', action='store')
+parser.add_argument('--ref', action='store')
+parser.add_argument('--out', action='store')
+
+args = parser.parse_args()
+
+def main(args):
+ data_manager_entry = {}
+ data_manager_entry['value'] = args.dbkey.lower()
+ data_manager_entry['name'] = args.dbkey
+ data_manager_entry['path'] = '.'
+ data_manager_entry['ref'] = args.ref
+ data_manager_entry['provider'] = args.provider
+ data_manager_json = dict(data_tables=dict(gene_sets=data_manager_entry))
+ params = json.loads(open(args.out).read())
+ target_directory = params['output_data'][0]['extra_files_path']
+ os.mkdir(target_directory)
+ output_path = os.path.join(os.getcwd(), 'featurecount_gxf')
+ for filename in os.listdir(output_path):
+ shutil.move(os.path.join(output_path, filename), target_directory)
+ file(args.output, 'w').write(json.dumps(data_manager_json))
+
+if __name__ == '__main__':
+ main(args)
diff -r 000000000000 -r 5ef1c072f07c gffdm/data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gffdm/data_manager_conf.xml Sun Jun 26 16:53:36 2016 -0400
@@ -0,0 +1,21 @@
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 5ef1c072f07c gffdm/tool-data/gene_sets.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gffdm/tool-data/gene_sets.loc.sample Sun Jun 26 16:53:36 2016 -0400
@@ -0,0 +1,39 @@
+# This is a sample file distributed with Galaxy that enables tools
+# to use gene/exon annotations in the GFF/GTF format. You will need
+# to add all the gene set annotations in this configuration file.
+# Because of this file, galaxy tools are able to access gene annotations
+# provided as GFF / GTF files by selecting on:
+# - Priorty (defined by the order in the file)
+# - Provider
+# - dbkey (reference genome id)
+#
+# The gene_sets.loc file syntax is:
+#
+# *optional
+#
+# Please ensure maximally one TAB (\t) between two columns!
+# ---------------------------------------------------------
+#
+# 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 000000000000 -r 5ef1c072f07c gffdm/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gffdm/tool_data_table_conf.xml.sample Sun Jun 26 16:53:36 2016 -0400
@@ -0,0 +1,8 @@
+
+
+
+
+ value, dbkey, path, provider, ref
+
+
+
diff -r 000000000000 -r 5ef1c072f07c gffdm/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gffdm/tool_dependencies.xml Sun Jun 26 16:53:36 2016 -0400
@@ -0,0 +1,9 @@
+
+
+
+ $REPOSITORY_INSTALL_DIR
+
+
+
+
+