Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 54:b60b0a9523db draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit c003994256543a5a4e99a1909135cce4f9b61692-dirty
| author | dfornika |
|---|---|
| date | Fri, 10 May 2019 20:34:55 -0400 |
| parents | 21cd25cc1ab2 |
| children | 40ea0695a0a0 |
| files | data_manager/kraken2_build_database.py data_manager/kraken2_build_database.xml |
| diffstat | 2 files changed, 9 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/kraken2_build_database.py Wed May 08 18:49:14 2019 -0400 +++ b/data_manager/kraken2_build_database.py Fri May 10 20:34:55 2019 -0400 @@ -124,6 +124,8 @@ now + ")" ]) + database_path = database_value + # download the minikraken2 data src = urlopen( 'ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_%s_8GB_201904_UPDATE.tgz' @@ -133,7 +135,11 @@ shutil.copyfileobj(src, dst) # unpack the downloaded archive to the target directory with tarfile.open('tmp_data.tar.gz', 'r:gz') as fh: - fh.extractall(target_directory) + for member in fh.getmembers(): + if member.isreg(): + member.name = os.path.basename(member.name) + fh.extract(member, os.path.join(target_directory, database_path)) + data_table_entry = { 'data_tables': { @@ -141,7 +147,7 @@ { "value": database_value, "name": database_name, - "path": database_value, + "path": database_path, } ] }
--- a/data_manager/kraken2_build_database.xml Wed May 08 18:49:14 2019 -0400 +++ b/data_manager/kraken2_build_database.xml Fri May 10 20:34:55 2019 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="kraken2_build_database" name="Kraken2 Database Builder" tool_type="manage_data" version="2.0.8_beta"> +<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta"> <macros> <xml name="common_params"> <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />