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.

Sign up for GitHub

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

Jump to bottom

[MRG] support local genome collections (including private genomes) #130

Merged
merged 66 commits into from
Jan 17, 2022
Merged

[MRG] support local genome collections (including private genomes) #130

merged 66 commits into from
Jan 17, 2022

Commits on Jan 6, 2022

  1. rename rule to sourmash_prefetch_wc

    @ctb
    ctb committed Jan 6, 2022
    Configuration menu
    Copy the full SHA
    5e4d7d0 View commit details
    Browse the repository at this point in the history

  2. start using {outdir}/genomes/

    @ctb
    ctb committed Jan 6, 2022
    Configuration menu
    Copy the full SHA
    858e966 View commit details
    Browse the repository at this point in the history

Commits on Jan 7, 2022

  1. swizzle up config to allowprivate_databases and genbank_databases, etc.

    @ctb
    ctb committed Jan 7, 2022
    Configuration menu
    Copy the full SHA
    238f194 View commit details
    Browse the repository at this point in the history

  2. more progress: copying private genomes around

    @ctb
    ctb committed Jan 7, 2022
    Configuration menu
    Copy the full SHA
    c17a8b5 View commit details
    Browse the repository at this point in the history

Commits on Jan 8, 2022

  1. combine listing private and genbank genomes - seems to work\!

    @ctb
    ctb committed Jan 8, 2022
    Configuration menu
    Copy the full SHA
    692e4fd View commit details
    Browse the repository at this point in the history

  2. simplify the ListGenomes stuff

    @ctb
    ctb committed Jan 8, 2022
    Configuration menu
    Copy the full SHA
    aa3641f View commit details
    Browse the repository at this point in the history

  3. it's aliiiiiiiive

    @ctb
    ctb committed Jan 8, 2022
    Configuration menu
    Copy the full SHA
    5ef6e33 View commit details
    Browse the repository at this point in the history

  4. remove genbank accession requirement

    @ctb
    ctb committed Jan 8, 2022
    Configuration menu
    Copy the full SHA
    5c70c56 View commit details
    Browse the repository at this point in the history

  5. remove genbank from most filenames, rules

    @ctb
    ctb committed Jan 8, 2022
    Configuration menu
    Copy the full SHA
    766cdd5 View commit details
    Browse the repository at this point in the history

  6. rename minimap to mapping; add clean_gather

    @ctb
    ctb committed Jan 8, 2022
    Configuration menu
    Copy the full SHA
    b3eb9d8 View commit details
    Browse the repository at this point in the history

  7. updated to properly (?) use checkpoints throughout

    @ctb
    ctb committed Jan 8, 2022
    Configuration menu
    Copy the full SHA
    efc78c1 View commit details
    Browse the repository at this point in the history

  8. tests pass locally

    @ctb
    ctb committed Jan 8, 2022
    Configuration menu
    Copy the full SHA
    4deab0a View commit details
    Browse the repository at this point in the history

  9. fix typo

    @ctb
    ctb committed Jan 8, 2022
    Configuration menu
    Copy the full SHA
    cb8bf37 View commit details
    Browse the repository at this point in the history

  10. add the beginnings of testing for private databases

    @ctb
    ctb committed Jan 8, 2022
    Configuration menu
    Copy the full SHA
    7b8e8d1 View commit details
    Browse the repository at this point in the history

Commits on Jan 10, 2022

  1. getting started

    @ctb
    ctb committed Jan 10, 2022
    Configuration menu
    Copy the full SHA
    ff04270 View commit details
    Browse the repository at this point in the history

Commits on Jan 11, 2022

  1. update all the things

    @ctb
    ctb committed Jan 11, 2022
    Configuration menu
    Copy the full SHA
    80fa463 View commit details
    Browse the repository at this point in the history

  2. [MRG] Change column names in intermediate CSVs. (#133) 

    * change column names

* remove old notebooks

* fix mistake
    @ctb
    ctb committed Jan 11, 2022
    Configuration menu
    Copy the full SHA
    79626e5 View commit details
    Browse the repository at this point in the history

Commits on Jan 12, 2022

  1. comments etc.

    @ctb
    ctb committed Jan 12, 2022
    Configuration menu
    Copy the full SHA
    453244e View commit details
    Browse the repository at this point in the history

  2. remove glob pattern, configure genbank_cache

    @ctb
    ctb committed Jan 12, 2022
    Configuration menu
    Copy the full SHA
    c63442f View commit details
    Browse the repository at this point in the history

  3. remove 'process' command

    @ctb
    ctb committed Jan 12, 2022
    Configuration menu
    Copy the full SHA
    06210b9 View commit details
    Browse the repository at this point in the history

  4. check for old config file params

    @ctb
    ctb committed Jan 12, 2022
    Configuration menu
    Copy the full SHA
    c8a9413 View commit details
    Browse the repository at this point in the history

  5. add important comment

    @ctb
    ctb committed Jan 12, 2022
    Configuration menu
    Copy the full SHA
    c729c71 View commit details
    Browse the repository at this point in the history

  6. actually remove 'process'

    @ctb
    ctb committed Jan 12, 2022
    Configuration menu
    Copy the full SHA
    6fc8d86 View commit details
    Browse the repository at this point in the history

  7. check for 'database_taxonomy' instead of 'taxonomies'

    @ctb
    ctb committed Jan 12, 2022
    Configuration menu
    Copy the full SHA
    9c5429f View commit details
    Browse the repository at this point in the history

  8. add trailing / in Makefile

    @ctb
    ctb committed Jan 12, 2022
    Configuration menu
    Copy the full SHA
    d381f6d View commit details
    Browse the repository at this point in the history

  9. add default taxonomies file to system.conf

    @ctb
    ctb committed Jan 12, 2022
    Configuration menu
    Copy the full SHA
    ea66682 View commit details
    Browse the repository at this point in the history

  10. fix test files

    @ctb
    ctb committed Jan 12, 2022
    Configuration menu
    Copy the full SHA
    1ac3c58 View commit details
    Browse the repository at this point in the history

  11. fix conf-private.yml

    @ctb
    ctb committed Jan 12, 2022
    Configuration menu
    Copy the full SHA
    eb83f2c View commit details
    Browse the repository at this point in the history

Commits on Jan 13, 2022

  1. initial commit

    @hackmd-deploy
    hackmd-deploy committed Jan 13, 2022
    Configuration menu
    Copy the full SHA
    a7e19cb View commit details
    Browse the repository at this point in the history

Commits on Jan 14, 2022

  1. start of doc/ subdirectory

    @ctb
    ctb committed Jan 14, 2022
    Configuration menu
    Copy the full SHA
    d0207ad View commit details
    Browse the repository at this point in the history

  2. add badge

    @hackmd-deploy
    hackmd-deploy committed Jan 14, 2022
    Configuration menu
    Copy the full SHA
    e2104a2 View commit details
    Browse the repository at this point in the history

  3. compleat first draft

    @hackmd-deploy
    hackmd-deploy committed Jan 14, 2022
    Configuration menu
    Copy the full SHA
    786dcc9 View commit details
    Browse the repository at this point in the history

  4. minor corrections

    @hackmd-deploy
    hackmd-deploy committed Jan 14, 2022
    Configuration menu
    Copy the full SHA
    116702e View commit details
    Browse the repository at this point in the history

  5. spell check

    @ctb
    ctb committed Jan 14, 2022
    Configuration menu
    Copy the full SHA
    d4666fd View commit details
    Browse the repository at this point in the history

Commits on Jan 15, 2022

  1. add picklists into the config (#136)

    @ctb
    ctb committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    28ea610 View commit details
    Browse the repository at this point in the history

  2. fix 'taxonomies' in test config; check that it's a list

    @ctb
    ctb committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    91949fb View commit details
    Browse the repository at this point in the history

  3. add comment

    @ctb
    ctb committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    19692c7 View commit details
    Browse the repository at this point in the history

  4. swipe from #97

    @hackmd-deploy
    hackmd-deploy committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    cd13ce5 View commit details
    Browse the repository at this point in the history

  5. Merge branch 'allow/private' of github.com:dib-lab/genome-grist into … 

    …allow/private
    @ctb
    ctb committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    69f2ea4 View commit details
    Browse the repository at this point in the history

  6. swipe getting started from #97

    @ctb
    ctb committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    883e4b1 View commit details
    Browse the repository at this point in the history

  7. update!

    @hackmd-deploy
    hackmd-deploy committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    683ea66 View commit details
    Browse the repository at this point in the history

  8. Apply suggestions from Taylor's docs review 

    Co-authored-by: Taylor Reiter <[email protected]>
    @ctb @taylorreiter
    ctb and taylorreiter committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    4d76d06 View commit details
    Browse the repository at this point in the history

  9. more update in re taylor's suggestions

    @hackmd-deploy
    hackmd-deploy committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    07786d4 View commit details
    Browse the repository at this point in the history

  10. more more update

    @hackmd-deploy
    hackmd-deploy committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    429d1ed View commit details
    Browse the repository at this point in the history

  11. even more update

    @hackmd-deploy
    hackmd-deploy committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    37f62f1 View commit details
    Browse the repository at this point in the history

  12. more update

    @hackmd-deploy
    hackmd-deploy committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    88ad402 View commit details
    Browse the repository at this point in the history

  13. more update

    @hackmd-deploy
    hackmd-deploy committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    ee8e371 View commit details
    Browse the repository at this point in the history

  14. fix help output for CLI

    @ctb
    ctb committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    459ee8b View commit details
    Browse the repository at this point in the history

  15. Merge branch 'allow/private' of github.com:dib-lab/genome-grist into … 

    …allow/private
    @ctb
    ctb committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    2d82031 View commit details
    Browse the repository at this point in the history

  16. configure mkdocs

    @ctb
    ctb committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    0ae63b7 View commit details
    Browse the repository at this point in the history

  17. clean it out

    @hackmd-deploy
    hackmd-deploy committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    1f9aa1c View commit details
    Browse the repository at this point in the history

  18. update gitignore

    @ctb
    ctb committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    b456353 View commit details
    Browse the repository at this point in the history

  19. add some figures

    @ctb
    ctb committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    96769e5 View commit details
    Browse the repository at this point in the history

  20. upd

    @ctb
    ctb committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    7878268 View commit details
    Browse the repository at this point in the history

  21. more figure adjustment

    @ctb
    ctb committed Jan 15, 2022
    Configuration menu
    Copy the full SHA
    7f743cc View commit details
    Browse the repository at this point in the history

Commits on Jan 16, 2022

  1. add badges

    @hackmd-deploy
    hackmd-deploy committed Jan 16, 2022
    Configuration menu
    Copy the full SHA
    5bcc054 View commit details
    Browse the repository at this point in the history

  2. simplify to single sourmash_dtabases; use 'local' instead of 'private'

    @ctb
    ctb committed Jan 16, 2022
    Configuration menu
    Copy the full SHA
    679c4ee View commit details
    Browse the repository at this point in the history

  3. update to 'local' instead of 'private'

    @hackmd-deploy
    hackmd-deploy committed Jan 16, 2022
    Configuration menu
    Copy the full SHA
    8900a7d View commit details
    Browse the repository at this point in the history

  4. fix extra backquote

    @hackmd-deploy
    hackmd-deploy committed Jan 16, 2022
    Configuration menu
    Copy the full SHA
    ee552bf View commit details
    Browse the repository at this point in the history

  5. more fix?

    @hackmd-deploy
    hackmd-deploy committed Jan 16, 2022
    Configuration menu
    Copy the full SHA
    0a0dc82 View commit details
    Browse the repository at this point in the history

  6. fix formatting

    @ctb
    ctb committed Jan 16, 2022
    Configuration menu
    Copy the full SHA
    03716aa View commit details
    Browse the repository at this point in the history

Commits on Jan 17, 2022

  1. add tax test

    @ctb
    ctb committed Jan 17, 2022
    Configuration menu
    Copy the full SHA
    c25c815 View commit details
    Browse the repository at this point in the history

  2. add test for picklist

    @ctb
    ctb committed Jan 17, 2022
    Configuration menu
    Copy the full SHA
    58bac94 View commit details
    Browse the repository at this point in the history

  3. switch SRR5950647_subset over to use local_databses_info 🎉

    @ctb
    ctb committed Jan 17, 2022
    Configuration menu
    Copy the full SHA
    d250a46 View commit details
    Browse the repository at this point in the history

  4. cleanup & commenting

    @ctb
    ctb committed Jan 17, 2022
    Configuration menu
    Copy the full SHA
    5515be8 View commit details
    Browse the repository at this point in the history

  5. add missing file

    @ctb
    ctb committed Jan 17, 2022
    Configuration menu
    Copy the full SHA
    367fbb1 View commit details
    Browse the repository at this point in the history