# HG changeset patch
# User davidvanzessen
# Date 1543589798 18000
# Node ID de3516853bde9b343d68faddfdf347af08d574fa
Uploaded
diff -r 000000000000 -r de3516853bde data_manager/fetch_vep_cache_data.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/fetch_vep_cache_data.py Fri Nov 30 09:56:38 2018 -0500
@@ -0,0 +1,54 @@
+import argparse
+import os
+import json
+import re
+import pprint
+import subprocess
+import sys
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser(description="Use VEP INSTALL.pl to download/process the cache for an assembly")
+ parser.add_argument("--output-file")
+ parser.add_argument("--output-dir")
+ parser.add_argument("--assembly")
+ args = parser.parse_args()
+
+ output_file = args.output_file
+ output_dir = args.output_dir
+ assembly = args.assembly
+ extra = args.assembly
+
+ with open(output_file) as output_file_handle:
+ params = json.loads(output_file_handle.read())
+
+ print(output_file)
+ print(output_dir)
+ print(assembly)
+ pprint.pprint(params)
+
+ if not os.path.exists(output_dir):
+ os.makedirs(output_dir)
+
+ vep_install_cmd = ["vep_install", "--NO_HTSLIB", "-a alcf", "--CACHEDIR", output_dir, "--SPECIES", assembly]
+ vep_install_cmd = "vep_install --NO_HTSLIB -a alcf --CACHEDIR {0} --SPECIES {1}".format(output_dir, assembly)
+ print("Running INSTALL.pl")
+ #print(" ".join(vep_install_cmd))
+ print(vep_install_cmd)
+ exit_code = subprocess.call(vep_install_cmd, cwd=output_dir, shell=True)
+ #process = subprocess.Popen(vep_install_cmd, shell=True, cwd=output_dir)
+
+ print(exit_code)
+
+ output_dict = dict(
+ data_tables=dict(
+ vep_cache_data=[{
+ "path": output_dir,
+ "dbkey": assembly,
+ "name": assembly,
+ "value": assembly
+ }]
+ )
+ )
+ with open(output_file, 'w') as output_file_handle:
+ output_file_handle.write(json.dumps(output_dict))
+ sys.exit(0)
\ No newline at end of file
diff -r 000000000000 -r de3516853bde data_manager/fetch_vep_cache_data.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/fetch_vep_cache_data.xml Fri Nov 30 09:56:38 2018 -0500
@@ -0,0 +1,37 @@
+
+
+ ensembl-vep
+
+ fetching
+
+
+python $__tool_directory__/fetch_vep_cache_data.py
+--output-file ${ out_file }
+--output-dir ${ out_file.extra_files_path }
+--assembly ${ dbkey }${ extra }
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ There is no help
+
+
\ No newline at end of file
diff -r 000000000000 -r de3516853bde data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Fri Nov 30 09:56:38 2018 -0500
@@ -0,0 +1,19 @@
+
+
+
+
+
+
+
+
diff -r 000000000000 -r de3516853bde tool-data/vep_cache_data.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/vep_cache_data.loc.sample Fri Nov 30 09:56:38 2018 -0500
@@ -0,0 +1,6 @@
+# VEP data cache location
+#
+# short name of the entry
+# galaxy ref key
+# display name of the entry
+# path to the directory of the cache dir
\ No newline at end of file