Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / dib-lab/genome-grist issues and pull requests

#315 - use directsketch to download genomes

Issue - State: open - Opened by ctb 13 days ago

#314 - WIP: Use `sourmash_plugin_branchwater`

Pull Request - State: closed - Opened by ctb 15 days ago

#313 - WIP: update genome-grist to modern days (Sep 2024)

Pull Request - State: open - Opened by ctb 2 months ago - 1 comment

#312 - modernize genome-grist :)

Issue - State: open - Opened by ctb 2 months ago

#311 - a passing thought on contaminated references

Issue - State: open - Opened by clb21565 4 months ago

#310 - Update pytest requirement from <7.5.0,>=5.1.2 to >=5.1.2,<8.1.0

Pull Request - State: open - Opened by dependabot[bot] 10 months ago
Labels: dependencies, python

#309 - Bump actions/cache from 3 to 4

Pull Request - State: open - Opened by dependabot[bot] 10 months ago
Labels: dependencies, github_actions

#308 - Bump lxml from 4.9.3 to 5.1.0

Pull Request - State: open - Opened by dependabot[bot] 11 months ago
Labels: dependencies, python

#307 - Bump lxml from 4.9.3 to 5.0.1

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies, python

#306 - Bump lxml from 4.9.3 to 5.0.0

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies, python

#305 - Bump pytest-dependency from 0.5.1 to 0.6.0

Pull Request - State: open - Opened by dependabot[bot] 11 months ago
Labels: dependencies, python

#304 - Bump lxml from 4.9.3 to 4.9.4

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies, python

#303 - Bump actions/setup-python from 4 to 5

Pull Request - State: open - Opened by dependabot[bot] 12 months ago
Labels: dependencies, github_actions

#302 - Bump conda-incubator/setup-miniconda from 2 to 3

Pull Request - State: open - Opened by dependabot[bot] 12 months ago
Labels: dependencies, github_actions

#301 - Bumping bcftools to 1.18 in bcftools.yml?

Issue - State: open - Opened by scunnac about 1 year ago

#300 - MRG: fix list in output doc

Pull Request - State: closed - Opened by ctb about 1 year ago

#299 - MRG: fix sketch command in configuring doc

Pull Request - State: closed - Opened by ctb about 1 year ago

#298 - Bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies, github_actions

#297 - revisit read naming - /1 and /2

Issue - State: open - Opened by ctb over 1 year ago

#296 - update sourmash command in docs to include *gz on configuring page

Issue - State: closed - Opened by jessicalumian over 1 year ago - 1 comment

#295 - switch to using `get-some-ncbi-genomes`

Issue - State: open - Opened by ctb over 1 year ago

#293 - fix documentation site to be better/nicer

Issue - State: open - Opened by ctb over 1 year ago

#292 - Bump lxml from 4.9.2 to 4.9.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, python

#291 - prioritize genomes found in previous samples when running genome grist

Issue - State: open - Opened by clb21565 over 1 year ago - 2 comments

#290 - Bump snakemake from 7.25.0 to 7.30.1

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#289 - Update pytest requirement from <7.4.0,>=5.1.2 to >=5.1.2,<7.5.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, python

#288 - Bump snakemake from 7.25.0 to 7.29.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#287 - Bump snakemake from 7.25.0 to 7.28.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#286 - Bump snakemake from 7.25.0 to 7.28.2

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#285 - Bump snakemake from 7.25.0 to 7.28.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#284 - Insert a list of accessions into the `samples:` section of the `config.yml` file!

Issue - State: open - Opened by ccbaumler over 1 year ago - 1 comment
Labels: documentation, code

#283 - Using `--cluster` parameter to run jobs

Issue - State: open - Opened by ccbaumler over 1 year ago - 1 comment
Labels: documentation, enhancement, good first issue

#282 - Bump snakemake from 7.25.0 to 7.26.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#281 - Bump snakemake from 7.25.0 to 7.25.4

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#280 - Bump snakemake from 7.25.0 to 7.25.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#279 - Bump snakemake from 7.25.0 to 7.25.2

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#278 - Problem with grist output

Issue - State: open - Opened by marsfro over 1 year ago

#277 - add check to ignore genome(s) that cannot be up downloaded

Issue - State: open - Opened by bcpd over 1 year ago - 4 comments

#276 - Update pytest requirement from <7.3.0,>=5.1.2 to >=5.1.2,<7.4.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#275 - Update pandas, pytest, and sourmash requirements.

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, python

#274 - Bump snakemake from 7.24.2 to 7.25.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, python

#273 - Problem installing geome-grist & spacegraphcats

Issue - State: open - Opened by hehouts over 1 year ago - 2 comments

#272 - Bump snakemake from 7.24.0 to 7.24.2

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, python

#271 - Bump snakemake from 7.24.0 to 7.24.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#270 - MRG: Ignore DeprecationWarning from sourmash in tests.

Pull Request - State: closed - Opened by ctb almost 2 years ago

#269 - Bump snakemake from 7.20.0 to 7.24.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments
Labels: dependencies, python

#267 - Bump snakemake from 7.20.0 to 7.22.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#265 - Bump snakemake from 7.20.0 to 7.21.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#264 - Bump snakemake from 7.19.1 to 7.20.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, python

#263 - What should we benchmark?

Issue - State: open - Opened by ccbaumler almost 2 years ago - 1 comment

#261 - Bump snakemake from 7.18.2 to 7.19.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, python

#260 - Bump lxml from 4.9.1 to 4.9.2

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, python

#259 - [MRG] update ignore_ident code for later use too

Pull Request - State: closed - Opened by ctb almost 2 years ago

#258 - [MRG] update actions to make sure right version(s) are being used

Pull Request - State: closed - Opened by ctb almost 2 years ago

#257 - Bump actions/cache from 2 to 3

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments
Labels: dependencies, github_actions

#256 - [MRG] update github actions to use modern conda/caching

Pull Request - State: closed - Opened by ctb almost 2 years ago

#255 - [MRG] add code to support skipping genomes by ident

Pull Request - State: closed - Opened by ctb almost 2 years ago

#254 - [MRG] add pip check to GitHub actions

Pull Request - State: closed - Opened by ctb almost 2 years ago

#253 - [MRG] update snakemake version in `environment.yml`, & other minor fixes

Pull Request - State: closed - Opened by ctb almost 2 years ago

#252 - [MRG] add gh-pages deploy action

Pull Request - State: closed - Opened by ctb almost 2 years ago

#251 - [MRG] update sourmash and screed versions

Pull Request - State: closed - Opened by ctb almost 2 years ago

#250 - [MRG] run actions regularly

Pull Request - State: closed - Opened by ctb almost 2 years ago

#249 - Bump lxml from 4.6.4 to 4.9.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#248 - Update click requirement from <8,>=7 to >=7,<9

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, python

#247 - Update pytest requirement from ~=5.1.2 to >=5.1.2,<7.3.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, python

#246 - Bump snakemake from 6.12.3 to 7.18.2

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments
Labels: dependencies, python

#245 - Bump actions/checkout from 2 to 3

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, github_actions

#244 - Bump actions/setup-python from 1 to 4

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, github_actions

#243 - [MRG] add dependabot

Pull Request - State: closed - Opened by ctb almost 2 years ago

#242 - [MRG] update snakemake and sourmash versions

Pull Request - State: closed - Opened by ctb almost 2 years ago

#241 - Errors if genome-grist run on Marine metagenomes

Issue - State: open - Opened by jeanzzhao almost 2 years ago - 25 comments

#240 - filesystem latency error

Issue - State: open - Opened by jeanzzhao about 2 years ago - 8 comments

#239 - print out important snakemake args when invoking genome-grist --help

Issue - State: open - Opened by clb21565 about 2 years ago - 1 comment

#238 - improved documentation for configuring conf.yml

Issue - State: closed - Opened by clb21565 about 2 years ago - 6 comments

#237 - quickstart tutorial command throws attribute error

Issue - State: closed - Opened by clb21565 about 2 years ago - 5 comments

#236 - add printout of version information when running genome-grist

Issue - State: open - Opened by ctb about 2 years ago

#234 - draft release protocol for genome-grist

Issue - State: open - Opened by ctb about 2 years ago

#233 - [MRG] fix genome download rule

Pull Request - State: closed - Opened by ctb about 2 years ago

#232 - update docs from *.abundtrim.fq.gz to *.trim.fq.gz name

Issue - State: closed - Opened by jessicalumian about 2 years ago - 1 comment

#231 - explore myst-nb for notebooks

Issue - State: open - Opened by ctb about 2 years ago

#229 - [MRG] fix calculation of memory required for prefetch step.

Pull Request - State: closed - Opened by ctb about 2 years ago

#228 - are the various config files being read properly?

Issue - State: open - Opened by ctb about 2 years ago

#227 - rename `gather/` subfolder to `sourmash/`

Issue - State: open - Opened by ctb about 2 years ago
Labels: breaking

#226 - draft release notes for genome-grist v0.9.0

Issue - State: closed - Opened by ctb about 2 years ago - 1 comment

#223 - explore removing khmer as a dependency of the main workflow

Issue - State: open - Opened by ctb about 2 years ago
Labels: breaking

#222 - move `Snakefile` directly under `genome_grist/`

Issue - State: open - Opened by ctb about 2 years ago
Labels: breaking

#220 - checklist for people upgrading to genome-grist v0.9.0

Issue - State: closed - Opened by ctb about 2 years ago - 1 comment

#219 - [MRG] rename `avg_unique_mapped_coverage` to `effective_coverage`

Pull Request - State: closed - Opened by ctb about 2 years ago

#218 - [MRG] fix trim-low-abund ksize to match analysis ksize

Pull Request - State: closed - Opened by ctb about 2 years ago - 2 comments

#217 - rename `avg_unique_mapped_coverage` to `effective_coverage`.

Issue - State: closed - Opened by ctb about 2 years ago

#216 - error with prefetch not finding match between query and metagenome

Issue - State: closed - Opened by jessicalumian about 2 years ago - 3 comments