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lskatz wants to merge 145 commits intopaperlskatz/Kalamari:paperfrom provenancelskatz/Kalamari:provenanceCopy head branch name to clipboard

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Commits

Commits on Jun 17, 2021

• GitHub actions (#13)

  Show description for 8f196ab
  lskatz

  authored
  8f196ab

Commits on Jul 1, 2021

• Add files via upload

  SVN-PhD

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  cd9704e

• adding taxonomy_v3.5.1

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  0388be2

Commits on Jul 22, 2021

• More formats (#17)

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  lskatz

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  1a2044e

Commits on Jul 23, 2021

• Listeria unit testing (#18)

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  lskatz

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  c1b607a

• Merge branch 'master' of https://github.com/SVN-PhD/Kalamari

  lskatz

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  78b8807

• new parent id

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  8ef7191

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

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  b94f912

• reduced taxonomy

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  93b6c51

• testing v3.9.2

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Commits on Jul 28, 2021

• added parentid to plasmids

  lskatz

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  f487aef

• Updating some Yersinia taxid (#16)

  Show description for d320139
  SVN-PhD

  authored
  d320139

• Merge branch 'master' of https://github.com/lskatz/Kalamari

  lskatz

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  37ed1f1

• adding v3.9.3 taxonomy

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• m

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• Merge branch 'custom-taxdump'

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  ecd900d

• adding in Scott's Yersinia genomes

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• cleanup

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  e9bef09

• updated to correct src tax dir

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• Update unit-testing.yml

  lskatz

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  c1de0bb

Commits on Jul 29, 2021

• Create CITATION.cff (#20)

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  lskatz

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  33a41aa

• Kraken1 unit test (#21)

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  lskatz

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  fa462f7

• Database doc update (#22)

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  lskatz

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  6e25f2f

• mash database

  lskatz

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  9917015

Commits on Jul 30, 2021

• Define contributions (#23)

  Show description for 703eaa8
  lskatz

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  703eaa8

Commits on Jul 31, 2021

• mmseqs2 just for fun

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• m

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Commits on Aug 17, 2021

• Sepia

  lskatz

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Commits on Aug 20, 2021

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

  Show description for e68611f
  lskatz

  authored
  e68611f

• Build sepia (#25)

  Show description for cfda1c1
  lskatz

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  cfda1c1

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

  lskatz

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  32fe463

• Merge branch 'master' of https://github.com/lskatz/Kalamari

  lskatz

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  715c538

Commits on Feb 11, 2022

• Merge branch 'master' of https://github.com/lskatz/Kalamari

  lskatz

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  72ff3ad

Commits on Feb 22, 2022

• validate a kraken database better

  lskatz

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  ffd0378

Commits on Mar 8, 2022

• MIDAS

  lskatz

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• m

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• m

  lskatz

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Commits on May 4, 2022

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

  kapsakcj

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Commits on May 18, 2022

• Update chromosomes.tsv

  lskatz

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  bda35f6

• using GITHUB_PATH to solve CI problems

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• m

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• m

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• limit tests to target branches

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• jellyfish now in path

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• m

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• remove -x statement

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• allow this workflow to work on master

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  45834dd

• trying out taxonomy validator workflow

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  42403da

• remove kraken1 from testing on this branch

  lskatz

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  1f47227

• fix path to taxonomy

  lskatz

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  6826d39

• Fix ci (#31)

  Show description for 22ab700
  lskatz

  authored
  22ab700

• Merge branch 'master' of github.com:lskatz/Kalamari

  lskatz

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  9e182a4

• check file sizes after pulling down accessions

  lskatz

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  2abecab

• more debugging in the ci just in case

  lskatz

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  7ac9e6a

Commits on Dec 14, 2022

• change cryptosporidium parent taxids to cryptosporidium the genus

  lskatz

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  36e9128

Commits on Jan 13, 2023

• marged new kalamari download script

  lskatz

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  f03b97c

• upped the version

  lskatz

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  5ecf07e

Commits on Jun 14, 2023

• getExactTaxonomy.pl: better error messages

  lskatz

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  5d56ed0

Commits on Apr 10, 2024

• downloadKalamari.pl: add in retmax 1

  lskatz

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  c24cff5

Commits on Apr 11, 2024

• only accept one sequence per insdc accession

  lskatz

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  53af4ee

Commits on Apr 29, 2024

• script to download kalamari from source

  lskatz

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  197c711

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

  lskatz

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  5ec301f

• bash downloadKalamari.sh

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  16a92f3

• update to ubuntu 20

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• 2 cpus in test

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  dbae8b1

• add spreadsheet as a strategy variable

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• m

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• m

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• split jobs between runners

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• fix math

  lskatz

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  8dd8c2d

• adding more retries

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  88d5f65

• switch to 1 cpu for testing

  lskatz

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  47ea970

• bump tag to v5.3.0

  lskatz

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  ccd4ca2

Commits on Apr 30, 2024

• std output for downloadKalamari.sh

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  5ca8b82

• removed bioperl

  lskatz

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  54f70b9

• bump version; add more standard conda db location

  lskatz

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  29da55c

Commits on May 2, 2024

• trying to speed up downloads

  Show description for 78fef19
  lskatz

  committed
  78fef19

Commits on May 3, 2024

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

  lskatz

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  4f31101

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

  lskatz

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• m

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• remove edirect setup unit test

  lskatz

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  7d95383

• update unit tests

  lskatz

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  ed46b3a

• just two chunks of tests

  lskatz

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  585ed0f

• batch more

  lskatz

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  dd2abc2

• fix file sizes check

  lskatz

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  9bd58e9

• just make the damn thing work

  lskatz

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  6698e50

Commits on May 5, 2024

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

  lskatz

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  51fea40

Commits on May 9, 2024

• More proper build (#42)

  Show description for 8bdf873
  lskatz

  authored
  8bdf873

Commits on May 10, 2024

• fix a downloading bug where sed stalls

  lskatz

  committed
  43182f3

Commits on May 14, 2024

• update for compressed kalamari library and more efficient kraken builds

  lskatz

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  d71690e

Commits on May 15, 2024

• update download script

  lskatz

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  d61b28b

Commits on May 17, 2024

• Validate taxonomy (#43)

  Show description for e926b3d
  lskatz

  authored
  e926b3d

• Add genomes (#45) (#46)

  Show description for 1f91677
  lskatz

  authored
  1f91677

Commits on May 18, 2024

• init paper

  lskatz

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  f77f31d

• some revisions; taxonomy; downloading

  lskatz

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  c80df02

• swap example

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• references

  lskatz

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  10e2aab

• stole Joe's draft-pdf.yml

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• update to version 4 of artifacts

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• plasmids description

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  c253755

Commits on May 20, 2024

• ignore rendered manuscripts

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  2e53322

• some minor fixes; author affiliations; code examples

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  62e29d8

• added Shatavia; updated example

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• m

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• revisions from Jess

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• refs

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  ac3f1e4

• fix list that became italics

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  5da3f14

Commits on May 21, 2024

• updated Andrew's affiliation

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• plasmid defined species

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• gave a name to the JOSS rendering

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• try experimental docx file creation

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• try 2 with container

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• correct artifact Action

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• m

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• upload artifact v4

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• branch agnostic

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  6a24c1c

Commits on May 22, 2024

• try multiple formats; multiple uploads

  lskatz

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  10c466f

• fix some citations

  lskatz

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  6e62d80

• fixed Dr. Lauer's info

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  3253b8e

• remove format arg

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  05c5a74

• shatavia's orcid

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  28d1203

• added Rebecca's and Jess's orcids

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  64422a8

• updated DOIs

  lskatz

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  946d383

• fixed comment line

  lskatz

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  29f9d28

• added Entrez Edirect URL

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  25cee50

• more Entrez citation with help from CoPilot

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  c0efade

• Andrew's orcid

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  208b7d5

Commits on May 26, 2024

• misc

  lskatz

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Commits on May 31, 2024

• updated revisions from coauthors

  lskatz

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Commits on Jun 4, 2024

• entered Taylor's revisiosn

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  c072b70

• move Katie to acknowledgements due to her request

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Commits on Jul 10, 2024

• changes from cdc clearance process

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  e0455fe

• disable buggy docx creation

  lskatz

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  4e3036b

• fix blast+ formatting typo

  lskatz

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  417c345

Commits on Jul 15, 2024

• update entrez ref

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Commits on Aug 9, 2024

• MRA

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• MRA

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Commits on Aug 30, 2024

• misc

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Commits on Sep 3, 2024

• 500 words or less

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• nix example

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• abstract

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• abbreviate genera

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Commits on Sep 10, 2024

• another paper revision

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• added asm pandoc template

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Commits on Oct 22, 2024

• provenance

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