# HG changeset patch
# User greg
# Date 1656623223 0
# Node ID c31256419bf6854464168d1d0957aae7745aded4
Uploaded
diff -r 000000000000 -r c31256419bf6 .shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml Thu Jun 30 21:07:03 2022 +0000
@@ -0,0 +1,16 @@
+name: data_manager_dram_database_downloader
+owner: iuc
+description: DRAM for distilling microbial metabolism to automate the curation of microbiome function
+homepage_url: https://github.com/WrightonLabCSU/DRAM
+long_description: |
+ DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes
+ and VirSorter identified viral contigs. DRAM annotates MAGs and viral contigs using KEGG (if provided by the
+ user), UniRef90, PFAM, dbCAN, RefSeq viral, VOGDB and the MEROPS peptidase database as well as custom user
+ databases. DRAM is run in two stages. First an annotation step to assign database identifiers to gene and then a
+ distill step to curate these annotations into useful functional categories. Additionally viral contigs are further
+ analyzed during to identify potential AMGs. This is done via assigning an auxiliary score and flags representing the
+ confidence that a gene is both metabolic and viral.
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader
+type: unrestricted
+categories:
+- Data Managers
diff -r 000000000000 -r c31256419bf6 data_manager/data_manager_dram_download.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_dram_download.py Thu Jun 30 21:07:03 2022 +0000
@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+
+import datetime
+import json
+import os
+import subprocess
+import sys
+
+today = datetime.date.today()
+with open(sys.argv[1]) as fh:
+ params = json.load(fh)
+target_directory = params['output_data'][0]['extra_files_path']
+os.mkdir(target_directory)
+param_dict = params['param_dict']
+
+# Now DRAM-setup.py can be called to download the data.
+cmd = 'DRAM-setup.py prepare_database --dbcan_version %d --threads %d' % (param_dict['--dbcan_version'], param_dict['--threads'])
+if '--skip_uniref' in param_dict:
+ cmd = '%s --skip_uniref' % cmd
+else:
+ cmd = '%s --uniref_version %d' % param_dict['--uniref_version']
+if '--keep_database_files' in param_dict:
+ cmd = '%s --keep_database_files' % cmd
+
+subprocess.check_call(cmd, shell=True)
+
+# Prepare the metadata for the new data table record.
+data_manager_dict = {
+ 'data_tables': {
+ 'dram_versioned_databases': [
+ {
+ 'value': today.isoformat(),
+ 'version': param_dict['dram_db_version'],
+ 'name': 'DRAM databases version %s' % param_dict['dram_db_version'],
+ 'path': None
+ }
+ ]
+ }
+}
+
+# Save it to the json results file.
+with open(sys.argv[1], 'w') as fh:
+ json.dump(data_manager_dict, fh, sort_keys=True)
diff -r 000000000000 -r c31256419bf6 data_manager/data_manager_dram_download.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_dram_download.xml Thu Jun 30 21:07:03 2022 +0000
@@ -0,0 +1,39 @@
+
+ the annotation files required by the DRAM suite of tools
+
+ 1.3.5
+
+
+ dram
+
+
+python '$__tool_directory__/data_manager_dram_download.py'
+'${out_file}'
+--skip_uniref
+--uniref_version $uniref_version
+--dbcan_version $dbcan_version
+--keep_database_files
+--threads \${GALAXY_SLOTS:-10}
+
+
+
+
+
+
+
+
+
+
+
+
+
+This tool downloads downloads and processes DRAM databases for annotation and makes them available to
+corresponding versions of the DRAM suite of tools.
+
+See https://github.com/WrightonLabCSU/DRAM/wiki for details about DRAM.
+
+
+ 10.1093/nar/gkaa621
+
+
+
diff -r 000000000000 -r c31256419bf6 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Thu Jun 30 21:07:03 2022 +0000
@@ -0,0 +1,20 @@
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r c31256419bf6 test-data/dram_databases.loc
diff -r 000000000000 -r c31256419bf6 tool-data/dram_databases.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/dram_databases.loc.sample Thu Jun 30 21:07:03 2022 +0000
@@ -0,0 +1,3 @@
+## DRAM databases
+#Value Version Name Path
+#2022-07-04 1.3.5 DRAM annotations (2022-07-04) /depot/data2/galaxy/tool-data/dram_databases/1.3.5/2022-07-04
diff -r 000000000000 -r c31256419bf6 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Jun 30 21:07:03 2022 +0000
@@ -0,0 +1,8 @@
+
+
+
+ value, version, name, path
+
+
+
+
diff -r 000000000000 -r c31256419bf6 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Thu Jun 30 21:07:03 2022 +0000
@@ -0,0 +1,7 @@
+
+
+
+ value, version, name, path
+
+
+