Provenance #54
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* unit-testing actions * unit-testing actions * unit-testing actions * unit-testing actions * installing edirect * installing edirect * installing edirect * installing edirect * installing edirect * rm travis * edirect through apt * edirect through apt
* new files for individual genes and coordinates * m * new flag to include optional files with --and
* Listeria unit testing draft * m * debug * debug * debug * update kalamari script; add --and flags * kraken1 db * m * m * m * m * editing PATH * editing PATH * fixing src path * m * fixing installation dir * jellyfish1 * jellyfish1 * m * just two genomes * tree kraken * added threads 2 * added threads 2 * build kraken -x * work on disk in kraken * debug * trying out kraken2 * m * removed rebuild and work-on-disk * kraken report * kraken report * more inspection of kraken output * more inspection of kraken output * done with unit testing for now Co-authored-by: Lee Katz - Aspen <gzu2@cdc.gov>
* Add files via upload * adding taxonomy_v3.5.1
* Create CITATION.cff * Update CITATION.cff
* with fixed taxonomy, unit test kraken1 * shortened the minimizer length to 9 * kraken1 query * m * adding a query is $query statement Co-authored-by: Lee Katz - Aspen <gzu2@cdc.gov>
* with fixed taxonomy, unit test kraken1 * shortened the minimizer length to 9 * kraken1 query * m * adding a query is $query statement * Update DATABASES.md * added blast and ANI instructions * updated docs to reflect more comprehensive DATABASES.md * m Co-authored-by: Lee Katz - Aspen <gzu2@cdc.gov>
* validate taxonomy script * unit testing for taxonomy * unit testing for taxonomy * moved XXXXXX entries to a todo file * validating names.dmp and added new entries to make taxonomy more complete * Contributing.md doc * link to contributing.md * more description under contributions Co-authored-by: Lee Katz - Aspen <gzu2@cdc.gov>
Co-authored-by: Lee Katz - Aspen <gzu2@cdc.gov>
* fixed bacillus genus back to bacteria in the plasmids * sepia building v1 * m * sepia documentation and reference generation script * m Co-authored-by: Lee Katz - Aspen <gzu2@cdc.gov>
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