v5.7.2

Fixed a bug in downloadKalamari.sh

v5.7.1

(no code changes)

• bumped the version to trigger a zenodo DOI

v5.7.0

update genome list; stable efetching (#49)

* Add genomes (#45)

* Corynebacterium diphtheriae

* added Bifidobacterium adolenscentis

* replaced S. enterica IIIa; Added hops (Humulus lupulus)

* added a Citrobacter species

* m

* replaced repressed genome accession for B. faecium

* Esearch input (#47)

* Add genomes (#45) (#46)

* Corynebacterium diphtheriae

* added Bifidobacterium adolenscentis

* replaced S. enterica IIIa; Added hops (Humulus lupulus)

* added a Citrobacter species

* m

* replaced repressed genome accession for B. faecium

* remove random single quotes

* bump version

* helpful log messages

* v5.6.3

* make symlink to avoid naming mistakes

* check whether taxonkit is loaded

* use efetch -input

* fix tr bug

* Esearch input flag (#48)

* Add genomes (#45) (#46)

* Corynebacterium diphtheriae

* added Bifidobacterium adolenscentis

* replaced S. enterica IIIa; Added hops (Humulus lupulus)

* added a Citrobacter species

* m

* replaced repressed genome accession for B. faecium

* remove random single quotes

* bump version

* helpful log messages

* v5.6.3

* make symlink to avoid naming mistakes

* check whether taxonkit is loaded

* use efetch -input

* fix tr bug

* get latest edirect

* update installation instructions

* update installation instructions: fix PATH

* bring in other tests

* update installation method for search with unit-testing

* update installation method for search with kraken2

* debug the ls statement

* debug the ls statement

* debug the ls statement

* debug building taxonomy

* exclusive unit testing for taxonomy for right now

* install taxonkit

v5.6.0

Add genomes (#45) (#46)

* Corynebacterium diphtheriae

* added Bifidobacterium adolenscentis

* replaced S. enterica IIIa; Added hops (Humulus lupulus)

* added a Citrobacter species

* m

* replaced repressed genome accession for B. faecium

v5.4.1

What's Changed

• More proper build by @lskatz in #42

Full Changelog: v5.4.0...v5.5.0

• Scripts to build Kraken1, Kraken2
• Better unit tests
• Script to build taxonomy from diff
• Remove files outside of git versioning

v5.4.0

Make things slightly more compatible with bioconda like setting the version in the executable

v5.3.3

Making this release to coincide with the conda release

v5.3.1

std output for downloadKalamari.sh

v5.2.1

some minor CI changes and now --help gives exit code 0

v5.2

• validate taxonomy script updated
• Better documentation
  • main doc
  • MIDAS database
• Fixed Salmonella subspecies IV and VIII