Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 2:18523fd8bec9 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 9b4d704c147761201fa9f1450fcf5ba6871104d8-dirty
| author | dfornika |
|---|---|
| date | Wed, 27 Feb 2019 21:03:42 -0500 |
| parents | f9a7275b1cad |
| children | c8e9fda07f11 |
| files | data_manager/kraken2_standard_database_builder.xml |
| diffstat | 1 files changed, 4 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/kraken2_standard_database_builder.xml Wed Feb 27 20:48:06 2019 -0500 +++ b/data_manager/kraken2_standard_database_builder.xml Wed Feb 27 21:03:42 2019 -0500 @@ -7,16 +7,17 @@ <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> <command detect_errors="exit_code"> <![CDATA[ - #set $library_list = str($libraries).split(',') - mkdir kraken2-database && cd kraken2-database && + export KRAKEN2_DB_NAME="`date --iso-8601`_standard" && + mkdir kraken2_database && cd kraken2_database && kraken2-build \ --standard \ + --db ${KRAKEN2_DB_NAME} \ --threads ${GALAXY_SLOTS:-1} \ --kmer-len ${kmer_len} \ --minimizer-len ${minimizer_len} \ --minimizer-spaces ${minimizer_spaces} && cd .. && - python '$__tool_directory__/make_json.py' --db `date --iso-8601`_standard --out '${out_file}' + python '$__tool_directory__/make_json.py' --db ${KRAKEN2_DB_NAME} --out '${out_file}' ]]> </command> <inputs>