# HG changeset patch
# User galaxyp
# Date 1573490877 18000
# Node ID 48893cfa76a8c8edb67172d5aac8bf1991c5bf0b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
diff -r 000000000000 -r 48893cfa76a8 data_manager/data_manager_eggnog.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_eggnog.py Mon Nov 11 11:47:57 2019 -0500
@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import json
+import os.path
+import sqlite3
+import sys
+from sqlite3 import OperationalError
+
+
+def _get_db_version(sqlitedb_path):
+ version = '4.5'
+ try:
+ query = 'select version from version'
+ conn = sqlite3.connect(sqlitedb_path)
+ cur = conn.cursor()
+ cur.execute(query)
+ version = cur.fetchone()[0]
+ except OperationalError as e:
+ print('Assuming eggnog version %s because %s %s' %
+ (version, sqlitedb_path, e), file=sys.stderr)
+ return version
+
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument('--config_file')
+ parser.add_argument('--install_path')
+ parser.add_argument('--dbs', default='')
+ args = parser.parse_args()
+
+ eggnog_db_path = os.path.join(args.install_path, 'eggnog.db')
+ if not os.path.exists(eggnog_db_path):
+ print('Can not open: %s' % eggnog_db_path, file=sys.stderr)
+ exit(1)
+ db_version = _get_db_version(eggnog_db_path)
+
+ # params = json.loads(open(args.config_file).read())
+ dm_dict = {}
+ dm_dict['data_tables'] = dm_dict.get('data_tables', {})
+ data_table = 'eggnog_mapper_db'
+ dm_dict['data_tables'][data_table]\
+ = dm_dict['data_tables'].get(data_table, [])
+ data_table_entry = dict(value=db_version, name=db_version,
+ path=args.install_path)
+ dm_dict['data_tables'][data_table].append(data_table_entry)
+ data_table = 'eggnog_mapper_hmm_dbs'
+ dm_dict['data_tables'][data_table]\
+ = dm_dict['data_tables'].get(data_table, [])
+ if args.dbs:
+ dbs = [x.strip() for x in args.dbs.split(',')]
+ for db in dbs:
+ key = '%s_%s' % (db_version, db)
+ data_table_entry = dict(key=key, db_version=db_version,
+ value=db, name=db, path=db)
+ dm_dict['data_tables'][data_table].append(data_table_entry)
+
+ # save info to json file
+ open(args.config_file, 'wb').write(json.dumps(dm_dict))
+
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r 48893cfa76a8 data_manager/data_manager_eggnog.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_eggnog.xml Mon Nov 11 11:47:57 2019 -0500
@@ -0,0 +1,34 @@
+
+ eggnog data to a specified directory
+
+ eggnog_macros.xml
+
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+ ^/.*$
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diff -r 000000000000 -r 48893cfa76a8 data_manager/eggnog_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/eggnog_macros.xml Mon Nov 11 11:47:57 2019 -0500
@@ -0,0 +1,173 @@
+
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+ 1.0.3
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+
+ 10.1093/nar/gkv1248
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+ eggnog-mapper
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+ emapper.py --version
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diff -r 000000000000 -r 48893cfa76a8 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Mon Nov 11 11:47:57 2019 -0500
@@ -0,0 +1,21 @@
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diff -r 000000000000 -r 48893cfa76a8 test-data/cached_locally/eggnog.db
Binary file test-data/cached_locally/eggnog.db has changed
diff -r 000000000000 -r 48893cfa76a8 test-data/cached_locally/eggnog_mapper_db.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/eggnog_mapper_db.loc Mon Nov 11 11:47:57 2019 -0500
@@ -0,0 +1,2 @@
+#value name path
+4.5 eggNOG_4.5 ${__HERE__}
diff -r 000000000000 -r 48893cfa76a8 test-data/cached_locally/eggnog_mapper_hmm_dbs.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/eggnog_mapper_hmm_dbs.loc Mon Nov 11 11:47:57 2019 -0500
@@ -0,0 +1,2 @@
+#key db_version value name path
+4.5_ENOG411CB2I 4.5 ENOG411CB2I ENOG411CB2I ${__HERE__}/hmmdb_levels/ENOG411CB2I/ENOG411CB2I
diff -r 000000000000 -r 48893cfa76a8 tool-data/eggnog_mapper_db.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/eggnog_mapper_db.loc.sample Mon Nov 11 11:47:57 2019 -0500
@@ -0,0 +1,25 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of eggnog_mapper data files.
+#
+# eggnog-mapper requires the following files to be installed in the data directory:
+# https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz
+# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz
+# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz
+# In addition individual HMM DBs can be installed from:
+# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/
+# A complete diamond database is available from:
+# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz
+#
+# The python script download_eggnog_data.py,
+# included with eggnog_mapper, can be used to download the files to the correct directory
+#
+# The near-equivalence of columns "value" and "db" is needed for the tests to work,
+# and for the setting of --data_dir to the parent directory of eggnog.db
+# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky.
+# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases
+# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de,
+# value and db should be the same (in the example, both should be "thaNOG")
+#
+#
+#db_version name path
+#4.5.1 eggnog_4.5.1 /path/to/directory/that/contains/eggnog.db
diff -r 000000000000 -r 48893cfa76a8 tool-data/eggnog_mapper_hmm_dbs.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/eggnog_mapper_hmm_dbs.loc.sample Mon Nov 11 11:47:57 2019 -0500
@@ -0,0 +1,28 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of eggnog_mapper data files.
+#
+# eggnog-mapper requires the following files to be installed in the data directory:
+# https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz
+# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz
+# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz
+# In addition individual HMM DBs can be installed from:
+# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/
+# A complete diamond database is available from:
+# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz
+#
+# The python script download_eggnog_data.py,
+# included with eggnog_mapper, can be used to download the files to the correct directory
+#
+# The near-equivalence of columns "value" and "db" is needed for the tests to work,
+# and for the setting of --data_dir to the parent directory of eggnog.db
+# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky.
+# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases
+# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de,
+# value and db should be the same (in the example, both should be "thaNOG")
+#
+#
+#key db_version value name path
+#4.5.1_NOG 4.5.1 NOG Full eggNOG database (NOG)
+#4.5.1_euk 4.5.1 euk Eukaryotes (euk)
+#4.5.1_aproNOG 4.5.1 aproNOG Proteobacteria_alpha (aproNOG)
+#4.5.1_aproNOG 4.5.1 ENOG411CB2I ENOG411CB2I (custom) /path/to/custom/hmmdb/ENOG411CB2I
diff -r 000000000000 -r 48893cfa76a8 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Nov 11 11:47:57 2019 -0500
@@ -0,0 +1,11 @@
+
+
+
+
+ key,db_version,value,name,path
+
+
+
diff -r 000000000000 -r 48893cfa76a8 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Mon Nov 11 11:47:57 2019 -0500
@@ -0,0 +1,11 @@
+
+
+
+
+ key,db_version,value,name,path
+
+
+