# HG changeset patch
# User iuc
# Date 1520874463 14400
# Node ID 4ea70130da21a3b0e96bcab1555d8c1034901e89
Uploaded
diff -r 000000000000 -r 4ea70130da21 .shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml Mon Mar 12 13:07:43 2018 -0400
@@ -0,0 +1,19 @@
+categories:
+- Data Managers
+description: |
+ Motif database downloader for the MEME Suite, which allows the biologist to discover novel motifs in collections
+ of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses.
+homepage_url: http://meme-suite.org/meme_4.11.3/db/motifs
+long_description: |
+ Motif database downloader for the MEME Suite, which supports motif-based analysis of DNA, RNA and protein sequences.
+ It provides motif discovery algorithms using both probabilistic (MEME) and discrete models (MEME), which have
+ complementary strengths. It also allows discovery of motifs with arbitrary insertions and deletions (GLAM2).
+ In addition to motif discovery, the MEME Suite provides tools for scanning sequences for matches to motifs (FIMO,
+ MAST and GLAM2Scan), scanning for clusters of motifs (MCAST), comparing motifs to known motifs (Tomtom), finding
+ preferred spacings between motifs (SpaMo), predicting the biological roles of motifs (GOMo), measuring the positional
+ enrichment of sequences for known motifs (CentriMo), and analyzing ChIP-seq and other large datasets (MEME-ChIP).
+ The MEME Suite is comprised of a collection of tools that work together.
+name: data_manager_meme_motif_database_downloader
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_meme_motif_database_downloader
+type: unrestricted
diff -r 000000000000 -r 4ea70130da21 data_manager/data_manager_meme_motif_databases_downloader.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_meme_motif_databases_downloader.py Mon Mar 12 13:07:43 2018 -0400
@@ -0,0 +1,119 @@
+#!/usr/bin/env python
+#
+# Data manager for downloading MEME Motif Databases.
+import argparse
+import json
+import os
+import shutil
+import sys
+import tarfile
+import urllib2
+import zipfile
+
+DEFAULT_DATA_TABLE_NAMES = ["meme_motif_databases"]
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--description', dest='description', default=None, help='Description')
+parser.add_argument('--name', dest='name', help='Data table entry unique ID')
+parser.add_argument('--out_file', dest='out_file', help='JSON output file')
+parser.add_argument('--web_url', dest='web_url', help='URL for downloading MEME motif databases')
+
+args = parser.parse_args()
+
+def add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
+ data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
+ data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
+ data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
+ return data_manager_dict
+
+
+def make_directory(dir):
+ if not os.path.exists(dir):
+ os.makedirs(dir)
+
+
+def remove_directory(dir):
+ if os.path.exists(dir):
+ shutil.rmtree(dir)
+
+
+def extract_archive(file_path, work_directory):
+ if tarfile.is_tarfile(file_path):
+ fh = tarfile.open(file_path, 'r:*')
+ elif zipfile.is_zipfile(file_path):
+ fh = zipfile.ZipFile(file_path, 'r')
+ else:
+ return
+ fh.extractall(work_directory)
+
+
+def move_files(source_directory, target_directory):
+ # Move the files into defined output directory.
+ for filename in os.listdir(source_directory):
+ shutil.move(os.path.join(source_directory, filename), target_directory)
+
+
+def url_download(url, work_directory):
+ file_path = os.path.join(work_directory, os.path.basename(url))
+ src = None
+ dst = None
+ try:
+ req = urllib2.Request(url)
+ src = urllib2.urlopen(req)
+ dst = open(file_path, 'wb')
+ while True:
+ chunk = src.read(2**10)
+ if chunk:
+ dst.write(chunk)
+ else:
+ break
+ except Exception, e:
+ print >>sys.stderr, str(e)
+ finally:
+ if src:
+ src.close()
+ if dst:
+ dst.close()
+ return file_path
+
+
+def download(target_directory, web_url, description, data_table_names=DEFAULT_DATA_TABLE_NAMES):
+ data_manager_dict = {}
+ data_table_entry = {}
+ # Download the databases.
+ work_directory = os.path.abspath(os.path.join(os.getcwd(), 'meme_motif_databases'))
+ make_directory(work_directory)
+ file_path = url_download(web_url, work_directory)
+ extract_archive(file_path, work_directory)
+ os.remove(file_path)
+ # Move the database files into the defined output directory.
+ move_files(work_directory, target_directory)
+ remove_directory(work_directory)
+ # Populate the data_manager_dict with the database data entry.
+ for file_path in os.listdir(target_directory):
+ full_path = os.path.abspath(os.path.join(target_directory, file_path))
+ entry_name = "%s" % os.path.basename(file_path)
+ data_table_entry['value'] = entry_name
+ data_table_entry['name'] = entry_name
+ data_table_entry['path'] = full_path
+ data_table_entry['description'] = description
+ # Populate the data_manager_dict.
+ for data_table_name in data_table_names:
+ data_manager_dict = add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
+ return data_manager_dict
+
+params = json.loads(open(args.out_file).read())
+target_directory = params['output_data'][0]['extra_files_path']
+make_directory(target_directory)
+
+if args.description is None:
+ description = ''
+else:
+ description = args.description.strip()
+
+# Get the databases.
+data_manager_dict = download(target_directory, args.web_url, description)
+# Write the JSON output dataset.
+fh = open(args.out_file, 'wb')
+fh.write(json.dumps(data_manager_dict))
+fh.close()
diff -r 000000000000 -r 4ea70130da21 data_manager/data_manager_meme_motif_databases_downloader.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_meme_motif_databases_downloader.xml Mon Mar 12 13:07:43 2018 -0400
@@ -0,0 +1,45 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. class:: infomark
+
+**What it does**
+
+This tool fetches MEME motif databases used by some of the MEME Galaxy tools and populates the meme_motif_databases
+data table. The databases can be imported using a URL, and an optional description can be provided that will appear
+next to the database file name in the data table entry.
+
+MEME Motif Databases can be downloaded using this URL:
+
+ * December, 2017: http://meme-suite.org/meme-software/Databases/motifs/motif_databases.12.17.tgz
+
+
+
+
+ 10.1093/bioinformatics/btr064
+
+
+
diff -r 000000000000 -r 4ea70130da21 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Mon Mar 12 13:07:43 2018 -0400
@@ -0,0 +1,20 @@
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 4ea70130da21 tool-data/meme_motif_database.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/meme_motif_database.loc.sample Mon Mar 12 13:07:43 2018 -0400
@@ -0,0 +1,3 @@
+## MEME Motif Databases
+#Value Name Path Description
+#2017_12 2017_12 /meme_motif_databases/2017_12 December 2017
diff -r 000000000000 -r 4ea70130da21 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Mar 12 13:07:43 2018 -0400
@@ -0,0 +1,6 @@
+
+
+ value, name, path, description
+
+
+