fixed bacillus genus back to bacteria in the plasmids #24
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lskatz
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Nov 5, 2024
Co-authored-by: Lee Katz - Aspen <gzu2@cdc.gov>
lskatz
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Nov 5, 2024
* 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 <gzu2@cdc.gov> * 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 <gzu2@cdc.gov> * 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 <gzu2@cdc.gov> * 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 <gzu2@cdc.gov> * mmseqs2 just for fun * m * Sepia * fixed bacillus genus back to bacteria in the plasmids (#24) Co-authored-by: Lee Katz - Aspen <gzu2@cdc.gov> * 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 <gzu2@cdc.gov> * 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 <svn.phd@gmail.com> Co-authored-by: Scott Nguyen <15314705+SVN-PhD@users.noreply.github.com> Co-authored-by: Curtis Kapsak <kapsakcj@gmail.com>
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