# HG changeset patch
# User iuc
# Date 1451404709 18000
# Node ID 7848037cb7019cad803bedd919d7881ec05d4c91
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
diff -r 000000000000 -r 7848037cb701 data_manager/data_manager_gemini_download.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_gemini_download.py Tue Dec 29 10:58:29 2015 -0500
@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+
+import sys
+import os
+import json
+import shlex
+import datetime
+import subprocess
+
+def main():
+
+ today = datetime.date.today()
+ params = json.loads( open( sys.argv[1] ).read() )
+ target_directory = params[ 'output_data' ][0]['extra_files_path']
+ os.mkdir( target_directory )
+ cmd = "gemini --annotation-dir %s update --dataonly %s %s" % (target_directory, params['param_dict']['gerp_bp'], params['param_dict']['cadd'] )
+ ret = subprocess.check_call( cmd, shell=True )
+ data_manager_dict = {
+ 'data_tables':
+ {'gemini_databases': [
+ {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() }
+ ]
+ }
+ }
+
+ #save info to json file
+ with open( sys.argv[1], 'wb' ) as out:
+ out.write( json.dumps( data_manager_dict ) )
+
+if __name__ == "__main__":
+ main()
+
diff -r 000000000000 -r 7848037cb701 data_manager/data_manager_gemini_download.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_gemini_download.xml Tue Dec 29 10:58:29 2015 -0500
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+
+ Download a new database
+
+ gemini
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+ data_manager_gemini_download.py "$out_file"
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+This tool downloads the GEMINI databases.
+
+For details about this tool, please go to http://gemini.readthedocs.org
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+
+
+ 10.1371/journal.pcbi.1003153
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+
+
+
diff -r 000000000000 -r 7848037cb701 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Tue Dec 29 10:58:29 2015 -0500
@@ -0,0 +1,21 @@
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diff -r 000000000000 -r 7848037cb701 tool-data/gemini_databases.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gemini_databases.loc.sample Tue Dec 29 10:58:29 2015 -0500
@@ -0,0 +1,3 @@
+## GEMINI databases
+#Version dbkey Description
+#08_08_2014 hg19 Database (08-08-2014)
diff -r 000000000000 -r 7848037cb701 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Dec 29 10:58:29 2015 -0500
@@ -0,0 +1,7 @@
+
+
+ value, dbkey, name, path
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diff -r 000000000000 -r 7848037cb701 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Dec 29 10:58:29 2015 -0500
@@ -0,0 +1,6 @@
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