Repository revision
8:88e27e10b1ed

Repository 'arriba_get_filters'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/arriba_get_filters

Arriba Get Filters tool metadata
Miscellaneous
Arriba Get Filters
to history
arriba_get_filters
toolshed.g2.bx.psu.edu/repos/iuc/arriba_get_filters/arriba_get_filters/2.5.1+galaxy0
2.5.1+galaxy0
arriba -h | grep Version | sed 's/^.* //'
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/arriba_get_filters/arriba_get_filters/2.5.1+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/arriba_get_filters/arriba_get_filters/2.5.0+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/arriba_get_filters/arriba_get_filters/2.4.0+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/arriba_get_filters/arriba_get_filters/2.4.0+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/arriba_get_filters/arriba_get_filters/2.4.0+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/arriba_get_filters/arriba_get_filters/2.3.0+galaxy3
toolshed.g2.bx.psu.edu/repos/iuc/arriba_get_filters/arriba_get_filters/2.3.0+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/arriba_get_filters/arriba_get_filters/2.3.0+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/arriba_get_filters/arriba_get_filters/2.3.0+galaxy0
arriba_get_filters
Requirements (dependencies defined in the <requirements> tag set)
name version type
arriba 2.5.1 package
Additional information about this tool
BASE_DIR=\$(dirname \$(dirname `which arriba`)) &&
    REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` &&
    REF_DIR=\$(dirname \$REF_SCRIPT) &&
    REF_NAME=${arriba_reference_name.split('+')[0].replace('viral','')} &&
    echo \$REF_NAME &&
    cp `find \$REF_DIR -name 'blacklist_*' | grep -i \$REF_NAME` '$blacklist' && 
    cp `find \$REF_DIR -name 'known_fusions_*' | grep -i \$REF_NAME` '$known_fusions' &&
    cp `find \$REF_DIR -name 'protein_domains_*' | grep -i \$REF_NAME` '$protein_domains' &&
    cp `find \$REF_DIR -name 'cytobands_*' | grep -i \$REF_NAME` '$cytobands'
    #*
    cp "\$REF_DIR/blacklist_*${arriba_reference_name}*" '$blacklist' &&
    cp "\$REF_DIR/known_fusions_*${arriba_reference_name}*" '$known_fusions' &&
    cp "\$REF_DIR/protein_domains_*${arriba_reference_name}*" '$protein_domains' &&
    cp "\$REF_DIR/cytobands_*${arriba_reference_name}*" '$cytobands'
    *#
None
False
Functional tests
name inputs outputs required files
Test-1 arriba_reference_name: GRCh38
 name: value
 value