Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 61:bf6408089cbc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66c35bd1ec30e6cd16d16f3cc98c2c5b56533a48-dirty
| author | dfornika |
|---|---|
| date | Mon, 29 Jul 2019 15:53:28 -0400 |
| parents | 0e635abf01ff |
| children | 38c99b294264 |
| files | data_manager/kraken2_build_database.py |
| diffstat | 1 files changed, 21 insertions(+), 24 deletions(-) [+] |
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--- a/data_manager/kraken2_build_database.py Fri Jul 26 19:54:59 2019 -0400 +++ b/data_manager/kraken2_build_database.py Mon Jul 29 15:53:28 2019 -0400 @@ -83,15 +83,14 @@ subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) - args = [ - '--threads', str(kraken2_args["threads"]), - '--db', database_path - ] - if kraken2_args["clean"]: - args.append('--clean') - - subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + args = [ + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', database_path + ] + + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) data_table_entry = { 'data_tables': { @@ -197,15 +196,14 @@ subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) - args = [ - '--threads', str(kraken2_args["threads"]), - '--db', database_path - ] + if kraken2_args["clean"]: + args = [ + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', database_path + ] - if kraken2_args["clean"]: - args.append('--clean') - - subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) data_table_entry = { 'data_tables': { @@ -254,15 +252,14 @@ subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) - args = [ - '--threads', str(kraken2_args["threads"]), - '--db', custom_database_name - ] + if kraken2_args["clean"]: + args = [ + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', custom_database_name + ] - if kraken2_args["clean"]: - args.append('--clean') - - subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) data_table_entry = { 'data_tables': {