Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Provenance2 into paper #56

Merged
merged 168 commits into from
Nov 5, 2024
Merged

Provenance2 into paper #56

merged 168 commits into from
Nov 5, 2024

Conversation

lskatz
Copy link
Owner

@lskatz lskatz commented Nov 5, 2024

No description provided.

lskatz and others added 30 commits June 17, 2021 13:29
* 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 <[email protected]>
* 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 <[email protected]>
* 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]>
* 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]>
* 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]>
@lskatz lskatz merged commit 684bec6 into paper Nov 5, 2024
6 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants