Repository revision
4:6d7aef331be9

Repository 'data_manager_build_kraken_database'
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database

Kraken tool metadata
Miscellaneous
Kraken
database builder
kraken_database_builder
toolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/kraken_database_builder/1.1
1.1
kraken -version | awk '{print $NF}'
False
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/kraken_database_builder/1.1 (this tool)
toolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/kraken_database_builder/1.0.2
toolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/kraken_database_builder/1.0.1
toolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/kraken_database_builder/1.0.0
kraken_database_builder
Requirements (dependencies defined in the <requirements> tag set)
name version type
kraken 1.1 package
Additional information about this tool
#set $library_list = str($libraries).split(',')
        mkdir kraken-database && cd kraken-database &&
        kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db '${database_name}' &&
        #for $library in $library_list:
            #if str($library) != 'None':
                kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db '${database_name}' &&
            #end if
        #end for
        #for $fasta in $input_fasta:
            #if str($fasta) != 'None':
                kraken-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --add-to-library '$fasta' &&
            #end if
        #end for
        kraken-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} &&
        cd .. &&
        python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}'
    
    
None
False
False
Functional tests
No functional tests defined