# HG changeset patch
# User dvanzessen
# Date 1563267425 14400
# Node ID 3333d43a58581d694d9cb533f1f96ef154621c77
# Parent 166e1c2b8c35c133457c1ec68ba26d73bbf1edf9
Uploaded
diff -r 166e1c2b8c35 -r 3333d43a5858 data_manager/fetch_vep_cache_data.py
--- a/data_manager/fetch_vep_cache_data.py Mon Jul 15 09:37:13 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-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("--species")
- parser.add_argument("--species-type", choices=["ensembl", "refseq", "merged"], default="ensembl")
- args = parser.parse_args()
-
- output_file = args.output_file
- output_dir = args.output_dir
-
- species = args.species
- assembly = ""
-
- if species.startswith("homo_sapiens"):
- if species.endswith("37"):
- assembly = " --ASSEMBLY GRCh37"
- elif species.endswith("38"):
- assembly = " --ASSEMBLY GRCh38"
- else:
- print("Unknown human assembly")
- sys.exit(1)
- species = "homo_sapiens"
-
- species_type = args.species_type
- if species_type in ["refseq", "merged"]:
- species = "{0}_{1}".format(species, species_type)
-
- with open(output_file) as output_file_handle:
- params = json.loads(output_file_handle.read())
-
- print(output_file)
- print(output_dir)
- print(species)
- print(species_type)
- pprint.pprint(params)
-
- if not os.path.exists(output_dir):
- os.makedirs(output_dir)
-
- vep_install_cmd = "vep_install --NO_HTSLIB -a alcf --CACHEDIR {0} --SPECIES {1}{2}".format(output_dir, species, assembly)
-
- print("Running INSTALL.pl")
- print(vep_install_cmd)
- exit_code = subprocess.call(vep_install_cmd, cwd=output_dir, shell=True)
-
- print(exit_code)
-
- output_dict = dict(
- data_tables=dict(
- vep_cache_data=[{
- "value": species,
- "path": output_dir,
- "dbkey": args.species,
- "type": species_type,
- "name": "{0} ({1})".format(args.species, species_type)
- }]
- )
- )
- with open(output_file, 'w') as output_file_handle:
- output_file_handle.write(json.dumps(output_dict))
- sys.exit(exit_code)
\ No newline at end of file
diff -r 166e1c2b8c35 -r 3333d43a5858 data_manager/fetch_vep_cache_data.xml
--- a/data_manager/fetch_vep_cache_data.xml Mon Jul 15 09:37:13 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,185 +0,0 @@
-
-
- ensembl-vep
- perl-dbi
- perl-archive-zip
- perl-dbd-mysql
-
- fetching
-
-
-python $__tool_directory__/fetch_vep_cache_data.py
---output-file ${ out_file }
---output-dir ${ out_file.extra_files_path }
---species ${ species }
---species-type ${ species_type }
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diff -r 166e1c2b8c35 -r 3333d43a5858 data_manager_conf.xml
--- a/data_manager_conf.xml Mon Jul 15 09:37:13 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
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diff -r 166e1c2b8c35 -r 3333d43a5858 tool-data/vep_cache_data.loc.sample
--- a/tool-data/vep_cache_data.loc.sample Mon Jul 15 09:37:13 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-# VEP data cache location
-#
-# unique key of an entry (species_)
-# galaxy ref key
-# cache type, ensembl, refseq or merged
-# display name of the entry
-# path to the directory of the cache dir
\ No newline at end of file
diff -r 166e1c2b8c35 -r 3333d43a5858 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Mon Jul 15 09:37:13 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-
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- value, dbkey, type, name, path
-
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diff -r 166e1c2b8c35 -r 3333d43a5858 vep.xml
--- a/vep.xml Mon Jul 15 09:37:13 2019 -0400
+++ b/vep.xml Tue Jul 16 04:57:05 2019 -0400
@@ -1,19 +1,8 @@
ensembl-vep
- perl-dbi
- perl-archive-zip
- perl-dbd-mysql
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