# HG changeset patch
# User sh477
# Date 1646039849 0
# Node ID a3dba0440f082faa1922e8bcd9d6cb60300d6d34
# Parent 97cd72b5130e31667fa374042837d05878505bfb
Reformatting
diff -r 97cd72b5130e -r a3dba0440f08 .shed.yml
--- a/.shed.yml Wed Feb 23 12:26:11 2022 +0000
+++ b/.shed.yml Mon Feb 28 09:17:29 2022 +0000
@@ -1,11 +1,11 @@
-categories:
-- Data Managers
-description: Download and install annotation cache files for Ensembl VEP
-long_description: |
- This tool downloads given versions of VEP cache annotation files and makes
- them available to Ensembl VEP in Galaxy via the "vep_versioned_caches" data
- table.
-name: data_manager_vep_cache_downloader
-owner: sh477
-remote_repository_url:
+categories:
+- Data Managers
+description: Download and install annotation cache files for Ensembl VEP
+long_description: |
+ This tool downloads given versions of VEP cache annotation files and makes
+ them available to Ensembl VEP in Galaxy via the "vep_versioned_caches" data
+ table.
+name: data_manager_vep_cache_downloader
+owner: sh477
+remote_repository_url:
type: unrestricted
\ No newline at end of file
diff -r 97cd72b5130e -r a3dba0440f08 data_manager/data_manager_vep_cache_download.py
--- a/data_manager/data_manager_vep_cache_download.py Wed Feb 23 12:26:11 2022 +0000
+++ b/data_manager/data_manager_vep_cache_download.py Mon Feb 28 09:17:29 2022 +0000
@@ -1,56 +1,56 @@
-#!/usr/bin/env python
-
-import datetime
-import json
-import os
-import re
-from urllib.request import urlretrieve
-import sys
-import tarfile
-
-
-def main():
- # Read in given out_file and create target directory for file download
- with open(sys.argv[1]) as fh:
- params = json.load(fh)
- target_directory = params['output_data'][0]['extra_files_path']
- os.mkdir(target_directory)
-
- # Process parameters for metadata and file download
- url = params['param_dict']['url'].rstrip("/") + "/" + params['param_dict']['file_name'].lstrip("/")
- m = re.search(r"_([^_]*?)_vep_(\d+?)_", params['param_dict']['file_name'])
- version = str(m.group(2))
- cache_type = m.group(1) if m.group(1) == "merged" or m.group(1) == "refseq" else "default"
-
- # Download and extract given cache archive, remove archive afterwards
- final_file, headers = urlretrieve(url, os.path.join(target_directory, params['param_dict']['file_name']))
- tar = tarfile.open(final_file, "r:gz")
- tar.extractall(target_directory)
- tar.close()
- os.remove(final_file)
-
- # Construct metadata for the new data table entry
- data_manager_dict = {
- 'data_tables': {
- 'vep_versioned_caches': [
- {
- 'value': params['param_dict']['file_name'].strip(".tar.gz"),
- 'dbkey': params['param_dict']['dbkey'],
- 'version': version,
- 'cachetype': cache_type,
- 'name': params['param_dict']['display_name'],
- 'path': './%s' % params['param_dict']['file_name'].strip(".tar.gz")
- }
- ]
- }
- }
-
- #assert 42 == 0, str(data_manager_dict)
-
- # Save metadata to out_file
- with open(sys.argv[1], 'w') as fh:
- json.dump(data_manager_dict, fh, sort_keys=True)
-
-
-if __name__ == "__main__":
- main()
+#!/usr/bin/env python
+
+import datetime
+import json
+import os
+import re
+from urllib.request import urlretrieve
+import sys
+import tarfile
+
+
+def main():
+ # Read in given out_file and create target directory for file download
+ with open(sys.argv[1]) as fh:
+ params = json.load(fh)
+ target_directory = params['output_data'][0]['extra_files_path']
+ os.mkdir(target_directory)
+
+ # Process parameters for metadata and file download
+ url = params['param_dict']['url'].rstrip("/") + "/" + params['param_dict']['file_name'].lstrip("/")
+ m = re.search(r"_([^_]*?)_vep_(\d+?)_", params['param_dict']['file_name'])
+ version = str(m.group(2))
+ cache_type = m.group(1) if m.group(1) == "merged" or m.group(1) == "refseq" else "default"
+
+ # Download and extract given cache archive, remove archive afterwards
+ final_file, headers = urlretrieve(url, os.path.join(target_directory, params['param_dict']['file_name']))
+ tar = tarfile.open(final_file, "r:gz")
+ tar.extractall(target_directory)
+ tar.close()
+ os.remove(final_file)
+
+ # Construct metadata for the new data table entry
+ data_manager_dict = {
+ 'data_tables': {
+ 'vep_versioned_caches': [
+ {
+ 'value': params['param_dict']['file_name'].strip(".tar.gz"),
+ 'dbkey': params['param_dict']['dbkey'],
+ 'version': version,
+ 'cachetype': cache_type,
+ 'name': params['param_dict']['display_name'],
+ 'path': './%s' % params['param_dict']['file_name'].strip(".tar.gz")
+ }
+ ]
+ }
+ }
+
+ #assert 42 == 0, str(data_manager_dict)
+
+ # Save metadata to out_file
+ with open(sys.argv[1], 'w') as fh:
+ json.dump(data_manager_dict, fh, sort_keys=True)
+
+
+if __name__ == "__main__":
+ main()
diff -r 97cd72b5130e -r a3dba0440f08 data_manager/data_manager_vep_cache_download.xml
--- a/data_manager/data_manager_vep_cache_download.xml Wed Feb 23 12:26:11 2022 +0000
+++ b/data_manager/data_manager_vep_cache_download.xml Mon Feb 28 09:17:29 2022 +0000
@@ -1,42 +1,42 @@
-
- ToDo:the cache files required by VEP
-
- python
-
-
- python '$__tool_directory__/data_manager_vep_cache_download.py' '$out_file'
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-This tool downloads given versions of VEP cache annotation files and makes them available to Ensembl VEP in Galaxy via the
-"vep_versioned_caches" data table. You should use the indexed version of the cache files and it is strongly recommended to
-use the cache files which version number matches the VEP version number. Note that for most genomes there are three versions
-of cache data available: default, refseq and merged (combining the former two). Choose the one suitable for your usage.
-
-A general introduction to the VEP cache and download links can be found on the official website:
-https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html
-
-
- 10.1186/s13059-016-0974-4
-
-
+
+ versioned annotation files for VEP
+
+ python
+
+
+ python '$__tool_directory__/data_manager_vep_cache_download.py' '$out_file'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+This tool downloads given versions of VEP cache annotation files and makes them available to Ensembl VEP in Galaxy via the
+"vep_versioned_caches" data table. You should use the indexed version of the cache files and it is strongly recommended to
+use the cache files which version number matches the VEP version number. Note that for most genomes there are three versions
+of cache data available: default, refseq and merged (combining the former two). Choose the one suitable for your usage.
+
+A general introduction to the VEP cache and download links can be found on the official website:
+https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html
+
+
+ 10.1186/s13059-016-0974-4
+
+
\ No newline at end of file
diff -r 97cd72b5130e -r a3dba0440f08 data_manager_conf.xml
--- a/data_manager_conf.xml Wed Feb 23 12:26:11 2022 +0000
+++ b/data_manager_conf.xml Mon Feb 28 09:17:29 2022 +0000
@@ -1,21 +1,21 @@
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
\ No newline at end of file
diff -r 97cd72b5130e -r a3dba0440f08 data_manager_conf.xml.sample
--- a/data_manager_conf.xml.sample Wed Feb 23 12:26:11 2022 +0000
+++ b/data_manager_conf.xml.sample Mon Feb 28 09:17:29 2022 +0000
@@ -1,12 +1,12 @@
-
-
-
- value, dbkey, version, cachetype, name, path
-
-
-
-
- value, name, len_path
-
-
-
+
+
+
+ value, dbkey, version, cachetype, name, path
+
+
+
+
+ value, name, len_path
+
+
+
\ No newline at end of file
diff -r 97cd72b5130e -r a3dba0440f08 data_manager_conf.xml.test
--- a/data_manager_conf.xml.test Wed Feb 23 12:26:11 2022 +0000
+++ b/data_manager_conf.xml.test Mon Feb 28 09:17:29 2022 +0000
@@ -1,12 +1,12 @@
-
-
-
- value, dbkey, version, cachetype, name, path
-
-
-
-
- value, name, len_path
-
-
-
+
+
+
+ value, dbkey, version, cachetype, name, path
+
+
+
+
+ value, name, len_path
+
+
+
\ No newline at end of file
diff -r 97cd72b5130e -r a3dba0440f08 test-data/dbkeys.loc
--- a/test-data/dbkeys.loc Wed Feb 23 12:26:11 2022 +0000
+++ b/test-data/dbkeys.loc Mon Feb 28 09:17:29 2022 +0000
@@ -1,3 +1,3 @@
#
hg38 Human hg38 a_path
-ce11 C. elegans ce11 a_path
+ce11 C. elegans ce11 a_path
\ No newline at end of file
diff -r 97cd72b5130e -r a3dba0440f08 test-data/vep_versioned_caches.loc
--- a/test-data/vep_versioned_caches.loc Wed Feb 23 12:26:11 2022 +0000
+++ b/test-data/vep_versioned_caches.loc Mon Feb 28 09:17:29 2022 +0000
@@ -1,2 +1,2 @@
-#
-#
+#
+#
diff -r 97cd72b5130e -r a3dba0440f08 tool-data/dbkeys.loc.sample
--- a/tool-data/dbkeys.loc.sample Wed Feb 23 12:26:11 2022 +0000
+++ b/tool-data/dbkeys.loc.sample Mon Feb 28 09:17:29 2022 +0000
@@ -1,1 +1,1 @@
-#
+#
\ No newline at end of file