# HG changeset patch
# User morinlab
# Date 1480893019 18000
# Node ID c6b7640b24e94803cf5d88f4d044a78f4304814c
Uploaded
diff -r 000000000000 -r c6b7640b24e9 fetch_ensembl_cache_data_manager/data_manager/data_manager_fetch_ensembl_cache.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fetch_ensembl_cache_data_manager/data_manager/data_manager_fetch_ensembl_cache.py Sun Dec 04 18:10:19 2016 -0500
@@ -0,0 +1,68 @@
+import sys
+import os
+import tempfile
+import optparse
+import subprocess
+
+from json import loads, dumps
+
+DEFAULT_DATA_TABLE_NAME = "ensembl_cache"
+
+def fetch_ensembl_cache(data_manager_dict, ensembl_vep_path, species, assembly, ensembl_version, params, target_directory, data_table_name):
+
+ perl_executable = '/'.join([ensembl_vep_path, "INSTALL.pl"])
+
+ commands = [ "perl" , perl_executable, "--AUTO", "cf", "--SPECIES", species, "--ASSEMBLY", assembly, "--CACHEDIR", target_directory ]
+
+ print commands
+
+ proc = subprocess.Popen( args=commands, shell=False, cwd=target_directory)
+ return_code = proc.wait()
+ if return_code:
+ print >> sys.stderr, "Error fetching ensembl cache"
+ sys.exit( return_code )
+
+ data_table_entry = dict(value='.'.join([species,assembly,ensembl_version]), name='.'.join([species,assembly,ensembl_version]), species=species, assembly=assembly, version=ensembl_version, path=target_directory )
+
+ _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
+
+def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
+ data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+ data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
+ data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
+ return data_manager_dict
+
+def main():
+
+ print >> sys.stderr, "Starting"
+
+ parser = optparse.OptionParser()
+ parser.add_option( '-i', '--organism_string', dest='input', action='store', type="string")
+ parser.add_option( '-e', '--ensembl_vep_path', dest='ensembl_vep_path', action='store', type='string')
+ (options, args) = parser.parse_args()
+
+ filename = args[0]
+
+ print >> sys.stderr, "What"
+ print >> sys.stderr, "When"
+
+ ensembl_vep_path = options.ensembl_vep_path
+ species = options.input.split("-")[0]
+ assembly = options.input.split("-")[1]
+ ensembl_version = 84
+
+ print >> sys.stderr, "hello"
+
+ params = loads( open( filename ).read() )
+ target_directory = params[ 'output_data' ][0]['extra_files_path']
+ os.mkdir( target_directory )
+ data_manager_dict = {}
+
+ #Fetch the Ensembl Cache
+ fetch_ensembl_cache( data_manager_dict, ensembl_vep_path, species, assembly, ensembl_version, params, target_directory, data_table_name=DEFAULT_DATA_TABLE_NAME )
+
+
+ #save info to json file
+ open( filename, 'wb' ).write( dumps( data_manager_dict ) )
+
+if __name__ == "__main__": main()
diff -r 000000000000 -r c6b7640b24e9 fetch_ensembl_cache_data_manager/data_manager/data_manager_fetch_ensembl_cache.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fetch_ensembl_cache_data_manager/data_manager/data_manager_fetch_ensembl_cache.xml Sun Dec 04 18:10:19 2016 -0500
@@ -0,0 +1,17 @@
+
+ fetcher
+
+ ensembl_vep
+
+
+ ensembl_vep_macros.xml
+
+
+ $__tool_directory__/data_manager_fetch_ensembl_cache.py "${out_file}" --organism_string $species_select.value --ensembl_vep_path "\$ENSEMBL_VEP_84_INSTALL_DIR"
+
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diff -r 000000000000 -r c6b7640b24e9 fetch_ensembl_cache_data_manager/data_manager/ensembl_vep_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fetch_ensembl_cache_data_manager/data_manager/ensembl_vep_macros.xml Sun Dec 04 18:10:19 2016 -0500
@@ -0,0 +1,76 @@
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diff -r 000000000000 -r c6b7640b24e9 fetch_ensembl_cache_data_manager/data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fetch_ensembl_cache_data_manager/data_manager_conf.xml Sun Dec 04 18:10:19 2016 -0500
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diff -r 000000000000 -r c6b7640b24e9 fetch_ensembl_cache_data_manager/tool-data/ensembl_cache.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fetch_ensembl_cache_data_manager/tool-data/ensembl_cache.loc Sun Dec 04 18:10:19 2016 -0500
@@ -0,0 +1,1 @@
+#
diff -r 000000000000 -r c6b7640b24e9 fetch_ensembl_cache_data_manager/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fetch_ensembl_cache_data_manager/tool_data_table_conf.xml.sample Sun Dec 04 18:10:19 2016 -0500
@@ -0,0 +1,6 @@
+
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+ value, name, species, assembly, version, path
+
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diff -r 000000000000 -r c6b7640b24e9 fetch_ensembl_cache_data_manager/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fetch_ensembl_cache_data_manager/tool_dependencies.xml Sun Dec 04 18:10:19 2016 -0500
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