Mercurial > repos > iuc > data_manager_gemini_database_downloader

changeset 2:345412d58d75 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_database_downloader commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author iuc
date Thu, 18 Feb 2016 08:49:06 -0500
parents a580422f6f1d
children 172815da3d41
files data_manager/data_manager_gemini_download.py data_manager/data_manager_gemini_download.xml tool_dependencies.xml
diffstat 3 files changed, 17 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_gemini_download.py	Tue Aug 26 19:58:38 2014 -0400
+++ b/data_manager/data_manager_gemini_download.py	Thu Feb 18 08:49:06 2016 -0500
@@ -10,19 +10,16 @@
 def main():
 
     today = datetime.date.today()
-    gemini_root_dir = os.environ['GEMINI_ROOT_DIR']
     params = json.loads( open( sys.argv[1] ).read() )
     target_directory = params[ 'output_data' ][0]['extra_files_path']
     os.mkdir( target_directory )
-    gemini_exec = os.path.join( gemini_root_dir, 'gemini', 'gemini', 'install-data.py' )
-    cmd = gemini_exec + " %s %s" % (' '.join( [params['param_dict']['gerp_bp'], params['param_dict']['cadd']] ), target_directory)
-    #cmd = gemini_exec + " --help > %s/foo.txt" % 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() } 
-                                        ] 
+    data_manager_dict = {
+                'data_tables':
+                    {'gemini_databases': [
+                            {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() }
+                                        ]
                     }
                 }
 
--- a/data_manager/data_manager_gemini_download.xml	Tue Aug 26 19:58:38 2014 -0400
+++ b/data_manager/data_manager_gemini_download.xml	Thu Feb 18 08:49:06 2016 -0500
@@ -1,32 +1,31 @@
-<tool id="data_manager_gemini_download" name="GEMINI Download" version="0.10.0" tool_type="manage_data">
+<tool id="data_manager_gemini_download" name="GEMINI Download" version="0.18.1" tool_type="manage_data">
     <description>Download a new database</description>
     <requirements>
-        <requirement type="package" version="0.10.0">gemini</requirement>
+        <requirement type="package" version="0.18.1">gemini</requirement>
     </requirements>
+    <stdio>
+        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
+        <exit_code range="1:"  level="fatal" description="Error" />
+    </stdio>
     <command interpreter="python">
         data_manager_gemini_download.py "$out_file"
     </command>
     <inputs>
-        <param name="cadd" type="boolean" truevalue="--extra cadd_score" falsevalue="" checked="True" 
+        <param name="cadd" type="boolean" truevalue="--extra cadd_score" falsevalue="" checked="True"
             label="Download CADD scores for GEMINI database annotation" help="(--extra cadd_score)"/>
-
-        <param name="gerp_bp" type="boolean" truevalue="--extra gerp_bp" falsevalue="" checked="True" 
+        <param name="gerp_bp" type="boolean" truevalue="--extra gerp_bp" falsevalue="" checked="True"
             label="Download GERP for GEMINI database annotation" help="(--extra gerp_bp)"/>
     </inputs>
     <outputs>
            <data name="out_file" format="data_manager_json" label="${tool.name}"/>
     </outputs>
-    <stdio>
-        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
-        <exit_code range="1:"  level="fatal" description="Error" />
-    </stdio>
     <tests>
     </tests>
     <help>
 
 This tool downloads the GEMINI databases.
 
-For details about this tool, please go to http://http://gemini.readthedocs.org
+For details about this tool, please go to http://gemini.readthedocs.org
 
     </help>
     <citations>
--- a/tool_dependencies.xml	Tue Aug 26 19:58:38 2014 -0400
+++ b/tool_dependencies.xml	Thu Feb 18 08:49:06 2016 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="gemini" version="0.10.0">
-        <repository changeset_revision="42c72725f879" name="package_gemini_0_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="gemini" version="0.18.1">
+        <repository changeset_revision="be869e11582f" name="package_gemini_0_18_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>