changeset 0:de3516853bde draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/fetch_vep_cache_data.py	Fri Nov 30 09:56:38 2018 -0500
@@ -0,0 +1,54 @@
+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("--assembly")
+    args = parser.parse_args()
+
+    output_file = args.output_file
+    output_dir = args.output_dir
+    assembly = args.assembly
+    extra = args.assembly
+
+    with open(output_file) as output_file_handle:
+        params = json.loads(output_file_handle.read())
+
+    print(output_file)
+    print(output_dir)
+    print(assembly)
+    pprint.pprint(params)
+
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+    
+    vep_install_cmd = ["vep_install", "--NO_HTSLIB", "-a alcf", "--CACHEDIR", output_dir, "--SPECIES", assembly]
+    vep_install_cmd = "vep_install --NO_HTSLIB -a alcf --CACHEDIR {0} --SPECIES {1}".format(output_dir, assembly)
+    print("Running INSTALL.pl")
+    #print(" ".join(vep_install_cmd))
+    print(vep_install_cmd)
+    exit_code = subprocess.call(vep_install_cmd, cwd=output_dir, shell=True)
+    #process = subprocess.Popen(vep_install_cmd, shell=True, cwd=output_dir)
+
+    print(exit_code)
+
+    output_dict = dict(
+        data_tables=dict(
+            vep_cache_data=[{
+                "path": output_dir,
+                "dbkey": assembly,
+                "name": assembly,
+                "value": assembly
+            }]
+        )
+    )
+    with open(output_file, 'w') as output_file_handle:
+        output_file_handle.write(json.dumps(output_dict))
+    sys.exit(0)
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/fetch_vep_cache_data.xml	Fri Nov 30 09:56:38 2018 -0500
@@ -0,0 +1,37 @@
+<tool id="fetch_vep_cache_data" name="VEP Cache" version="0.0.1" tool_type="manage_data">
+  <requirements>
+    <requirement type="package" version="94.5">ensembl-vep</requirement>
+  </requirements>
+  <description>fetching</description>
+  
+  <command detect_errors="exit_code">
+python $__tool_directory__/fetch_vep_cache_data.py 
+--output-file ${ out_file } 
+--output-dir ${ out_file.extra_files_path } 
+--assembly ${ dbkey }${ extra }
+  </command>
+  <inputs>
+    <param name="dbkey" type="select" label="Species">
+      <option value="homo_sapiens">Human</option>
+      <option value="mus_musculus">Mouse</option>
+    </param>
+    <param name="extra" type="select" label="Get the Ensembl, Refseq or merged Ensembl/Refseq">
+      <option value="" selected="true">Ensembl</option>
+      <option value="_refseq">Refseq</option>
+      <option value="_merged">Merged</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file" format="data_manager_json"/>
+  </outputs>
+  <!-- 
+  <tests>
+      <test>
+          DON'T FORGET TO DEFINE SOME TOOL TESTS
+      </test>
+  </tests>
+  -->
+  <help>
+  There is no help
+  </help>
+</tool>
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Fri Nov 30 09:56:38 2018 -0500
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<data_managers>
+    <data_manager tool_file="data_manager/fetch_vep_cache_data.xml" id="fetch_vep_cache_data">
+            <data_table name="vep_cache_data">
+                <output>
+                    <column name="value" />
+                    <column name="dbkey" />
+                    <column name="name" />
+                    <column name="path" output_ref="out_file" >
+                        <move type="directory">
+                            <source>${path}</source>
+                            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/seq/${path}</target>
+                        </move>
+                        <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/seq/${path}</value_translation>
+                    </column>
+                </output>
+            </data_table>
+    </data_manager>
+</data_managers>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/vep_cache_data.loc.sample	Fri Nov 30 09:56:38 2018 -0500
@@ -0,0 +1,6 @@
+# VEP data cache location
+# <value>    <dbkey>    <name>    <path>
+# <value> short name of the entry
+# <dbkey> galaxy ref key
+# <name> display name of the entry
+# <path> path to the directory of the cache dir
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