--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager.py	Tue Apr 04 17:50:05 2017 -0400
@@ -0,0 +1,74 @@
+import argparse
+import datetime
+import json
+import os
+import sys
+import uuid
+
+import requests
+from requests.exceptions import ContentDecodingError
+
+
+def url_download(url):
+    """Attempt to download gene annotation file from a given url
+    :param url: full url to gene annotation file
+    :type url: str.
+    :returns: name of downloaded gene annotation file
+    :raises: ContentDecodingError, IOError
+    """
+    response = requests.get(url=url, stream=True)
+
+    # Generate file_name
+    file_name = response.url.split("/")[-1]
+
+    block_size = 10 * 1024 * 1024  # 10MB chunked download
+    with open(file_name, 'w+') as f:
+        try:
+            # Good to note here that requests' iter_content() will
+            # automatically handle decoding "gzip" and "deflate" encoding
+            # formats
+            for buf in response.iter_content(block_size):
+                f.write(buf)
+        except (ContentDecodingError, IOError) as e:
+            sys.stderr.write("Error occured downloading reference file: %s"
+                             % e)
+            os.remove(file_name)
+
+    return file_name
+
+
+def main():
+    parser = argparse.ArgumentParser(description='Create data manager JSON.')
+    parser.add_argument('--out', dest='output', action='store',
+                        help='JSON filename')
+    parser.add_argument('--name', dest='name', action='store',
+                        default=uuid.uuid4(), help='Data table entry unique ID'
+                        )
+    parser.add_argument('--url', dest='url', action='store',
+                        help='Url to download gtf file from')
+
+    args = parser.parse_args()
+
+    work_dir = os.getcwd()
+
+    # Attempt to download gene annotation file from given url
+    gene_annotation_file_name = url_download(args.url)
+
+    # Update Data Manager JSON and write to file
+    data_manager_entry = {
+        'data_tables': {
+            'gff_gene_annotations': {
+                'value': str(datetime.datetime.now()),
+                'dbkey': str(args.name),
+                'name': gene_annotation_file_name,
+                'path': os.path.join(work_dir, gene_annotation_file_name)
+            }
+        }
+    }
+
+    with open(os.path.join(args.output), "w+") as f:
+        f.write(json.dumps(data_manager_entry))
+
+
+if __name__ == '__main__':
+    main()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/gene_annotation_fetcher.xml	Tue Apr 04 17:50:05 2017 -0400
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<tool id="gene_annotation_fetcher_data_manager" name="Gene Annotation Fetch" tool_type="manage_data" version="1.0.1">
+    <description>gene annotation fetcher</description>
+    <requirements>
+        <requirement type="package" version="2.13.0">requests</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+    <![CDATA[
+        python '$__tool_directory__/data_manager.py' --out '${out_file}'
+        #if $gene_annotation_url:
+            --url '${gene_annotation_url}'
+        #end if
+        #if $database_name:
+            --name '${database_name}'
+        #end if
+    ]]>
+    </command>
+    <inputs>
+        <param name="database_name" type="text" optional="true" label="Name for this database" help="Enter a unique identifier, or leave blank for today's date" />
+        <param name="gene_annotation_url" type="text" label="Enter URL for gene annotation files" />
+    </inputs>
+    <outputs>
+        <data format="data_manager_json" name="out_file" />
+    </outputs>
+    <help>
+    </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Tue Apr 04 17:50:05 2017 -0400
@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<data_managers>
+
+    <data_manager tool_file="data_manager/gene_annotation_fetcher.xml" id="gene_annotation_fetcher" version="1.0.0">
+        <data_table name="gff_gene_annotations">
+            <output>
+                <column name="value" />
+                <column name="dbkey" />
+                <column name="name" />
+                <column name="path" output_ref="out_file" >
+                    <move type="file">
+                        <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>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+
+</data_managers>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Apr 04 17:50:05 2017 -0400
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of gene annotation data -->
+    <table name="gff_gene_annotations" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/gene_annotation.loc" />
+    </table>
+</tables>
\ No newline at end of file