# HG changeset patch
# User dfornika
# Date 1564610886 14400
# Node ID f25264bb7d6d133b60128715f89c97952f91eb07
# Parent 0a2f97661db356ae0efb6242ac467ea9ffa0a28a
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_bracken_database/ commit 324b55b24e9d403b04a1cc6aba362b03bad98368-dirty
diff -r 0a2f97661db3 -r f25264bb7d6d data_manager/bracken_build_database.py
--- a/data_manager/bracken_build_database.py Fri Jul 26 17:18:22 2019 -0400
+++ b/data_manager/bracken_build_database.py Wed Jul 31 18:08:06 2019 -0400
@@ -25,7 +25,7 @@
database_name = database_name
- database_path = database_value
+ database_path = bracken_build_args['kraken_database']
try:
os.mkdir( os.path.join(target_directory, database_path) )
@@ -35,8 +35,7 @@
else:
raise
-
-
+
bracken_build_args_list = [
'-t', bracken_build_args['threads'],
'-k', bracken_build_args['kmer_len'],
@@ -46,12 +45,7 @@
subprocess.check_call(['bracken-build'] + bracken_build_args_list,
cwd=os.path.join(target_directory, database_path))
-
- bagit_args_list = [
- database_path,
- ]
- subprocess.call(['bagit.py'] + bagit_args_list, cwd=target_directory)
data_table_entry = {
"data_tables": {
@@ -59,7 +53,7 @@
{
"value": database_value,
"name": database_name,
- "path": os.path.join(database_path, 'data'),
+ "path": os.path.join(database_path),
}
]
}
diff -r 0a2f97661db3 -r f25264bb7d6d data_manager_conf.xml
--- a/data_manager_conf.xml Fri Jul 26 17:18:22 2019 -0400
+++ b/data_manager_conf.xml Wed Jul 31 18:08:06 2019 -0400
@@ -6,8 +6,8 @@
- #import os#${os.path.dirname($path)}
- bracken_databases/#import os#${os.path.dirname($path)}
+ ${path}
+ bracken_databases/${path}
${GALAXY_DATA_MANAGER_DATA_PATH}/bracken_databases/${path}
abspath