* 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 <[email protected]>

* GitHub actions (#13)

* 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

* Add files via upload

* adding taxonomy_v3.5.1

* More formats (#17)

* new files for individual genes and coordinates

* m

* new flag to include optional files with --and

* Listeria unit testing (#18)

* 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 <[email protected]>

* new parent id

* a get taxonomy script for a reduced set of dmp files

* reduced taxonomy

* testing v3.9.2

* added parentid to plasmids

* Updating some Yersinia taxid (#16)

* Add files via upload

* adding taxonomy_v3.5.1

* adding v3.9.3 taxonomy

* m

* adding in Scott's Yersinia genomes

* cleanup

* updated to correct src tax dir

* Update unit-testing.yml

* Create CITATION.cff (#20)

* Create CITATION.cff

* Update CITATION.cff

* Kraken1 unit test (#21)

* 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 <[email protected]>

* Database doc update (#22)

* 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 <[email protected]>

* mash database

* Define contributions (#23)

* 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 <[email protected]>

* mmseqs2 just for fun

* m

* Sepia

* fixed bacillus genus back to bacteria in the plasmids (#24)

Co-authored-by: Lee Katz - Aspen <[email protected]>

* Build sepia (#25)

* 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 <[email protected]>

* fixed a bug where the same fasta file would be downloaded twice and given the parent taxid in addition to its own

* validate a kraken database better

* MIDAS

* m

* m

* Update README.md with reqs and recs (#29)

* Update chromosomes.tsv

* using GITHUB_PATH to solve CI problems

* m

* m

* limit tests to target branches

* jellyfish now in path

* m

* remove -x statement

* allow this workflow to work on master

* trying out taxonomy validator workflow

* remove kraken1 from testing on this branch

* fix path to taxonomy

* Fix ci (#31)

* using GITHUB_PATH to solve CI problems

* m

* m

* limit tests to target branches

* jellyfish now in path

* m

* remove -x statement

* allow this workflow to work on master

* trying out taxonomy validator workflow

* remove kraken1 from testing on this branch

* fix path to taxonomy

* check file sizes after pulling down accessions

* more debugging in the ci just in case

* change cryptosporidium parent taxids to cryptosporidium the genus

* marged new kalamari download script

* upped the version

* getExactTaxonomy.pl: better error messages

* downloadKalamari.pl: add in retmax 1

* only accept one sequence per insdc accession

* script to download kalamari from source

* numcpus option added; new bash script to download and format

* bash downloadKalamari.sh

* update to ubuntu 20

* 2 cpus in test

* add spreadsheet as a strategy variable

* m

* m

* split jobs between runners

* fix math

* adding more retries

* switch to 1 cpu for testing

* bump tag to v5.3.0

* std output for downloadKalamari.sh

* removed bioperl

* bump version; add more standard conda db location

* trying to speed up downloads
rd conda db location

* vast speed increase with batch downloads; cleaned up chromosomes.tsv

* moved version information to the script from Makefile.PL; removed --and; won't make kraken db in shell script

* m

* remove edirect setup unit test

* update unit tests

* just two chunks of tests

* batch more

* fix file sizes check

* just make the damn thing work

* bash file uses local repo files instead of curl; default buffer size 100

* More proper build (#42)

* Building taxonomy (#38)

* building taxonomy files but this script will be deprecated right away

* deprecated

* script to build taxonomy with src files

* m

* move old taxonomy to deprecated

* remove old 'versioned' files outside of git versioning

* filter taxonomy script

* complete the taxonomy

* updated scripts for compiling databases

* dev branch testing

* fix lmono test a bit

* .

* Fix the taxonomy tests (#39)

* building taxonomy files but this script will be deprecated right away

* deprecated

* script to build taxonomy with src files

* m

* move old taxonomy to deprecated

* remove old 'versioned' files outside of git versioning

* filter taxonomy script

* complete the taxonomy

* updated scripts for compiling databases

* dev branch testing

* fix lmono test a bit

* .

* fix paths

* updated PATH

* updated PATH

* troubleshooting

* fix PATH again

* fix ls path

* remove that step

* updated tests to reflect build-taxonomy (#40)

* fix path to taxonomy files

* download and build taxonomy

* merge Listeria into Yersinia matrix

* m

* updated output directory as matrix.GENUS

* kraken1 tests patches

* m

* Fixed two more tests (#41)

* update yml

* query fallback

* debugging msg

* fix path to taxonomydb

* print first two lines of fasta files

* helpful cut statement

* remove head statement in last step

* bump version

* fix a downloading bug where sed stalls

* update for compressed kalamari library and more efficient kraken builds

* update download script

* Validate taxonomy (#43)

* validateTaxonomy update for just taxdirs; add 1 for filtered taxonomy; added DEBUG option for downloadKalamari.sh

* updated unit tests

* updated unit tests

* remove taxonomy stuff from downloadKalamari.sh

* fix validateTaxonomy syscall

* check on filtered tax in unit test

* 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

* init paper

* some revisions; taxonomy; downloading

* swap example

* references

* stole Joe's draft-pdf.yml

* update to version 4 of artifacts

* plasmids description

* ignore rendered manuscripts

* some minor fixes; author affiliations; code examples

* added Shatavia; updated example

* m

* revisions from Jess

* refs

* fix list that became italics

* updated Andrew's affiliation

* plasmid defined species

* gave a name to the JOSS rendering

* try experimental docx file creation

* try 2 with container

* correct artifact Action

* m

* upload artifact v4

* branch agnostic

* try multiple formats; multiple uploads

* fix some citations

* fixed Dr. Lauer's info

* remove format arg

* shatavia's orcid

* added Rebecca's and Jess's orcids

* updated DOIs

* fixed comment line

* added Entrez Edirect URL

* more Entrez citation with help from CoPilot

* Andrew's orcid

* misc

* remove random single quotes

* bump version

* helpful log messages

* v5.6.3

* updated revisions from coauthors

* entered Taylor's revisiosn

* move Katie to acknowledgements due to her request

* 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

* changes from cdc clearance process

* disable buggy docx creation

* fix blast+ formatting typo

* Change to MIT license

* Update README.md: remove CC license sticker

* update entrez ref

* MRA

* MRA

* misc

* 500 words or less

* nix example

* abstract

* abbreviate genera

* another paper revision

* added asm pandoc template

* provenance

* Leptospira interrogans => CP020414

* some progress

* downloadKalamari.sh: nuccleotideAcc bug fuxed

* v5.7.2

* another round of provenance

* cleared out the unknowns list

* fixed chromosomes with sources

* chromosomes

* try to run CI

* fix wildcard

* better named sources for each assembly

* polish this directory

* assembly-complete.gz

---------

Co-authored-by: Scott Nguyen <[email protected]>
Co-authored-by: Scott Nguyen <[email protected]>
Co-authored-by: Curtis Kapsak <[email protected]>