--- /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)
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