Ecosyste.ms: Issues

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

GitHub / spacegraphcats/spacegraphcats issues and pull requests

#515 - Bump codecov/codecov-action from 3 to 4

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

#514 - Bump actions/cache from 3 to 4

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

#513 - [MRG] Add chmod conditional for write access on bcalm.unitigs.db

Pull Request - State: open - Opened by ccbaumler 11 months ago - 1 comment

#512 - Error in `bcalm_catlas_prepare_input`

Issue - State: open - Opened by ccbaumler 11 months ago - 12 comments

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

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

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

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

#508 - Interpretation of first_doms.txt

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

#506 - Bump actions/checkout from 3 to 4

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

#505 - Bump snakemake from 7.30.1 to 7.30.2

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

#504 - Bump snakemake from 7.25.2 to 7.30.1

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

#503 - Bump snakemake from 7.25.2 to 7.30.0

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

#502 - Bump snakemake from 7.25.2 to 7.29.0

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

#501 - Bump snakemake from 7.25.2 to 7.28.3

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

#500 - Bump snakemake from 7.25.2 to 7.28.2

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

#499 - Bump snakemake from 7.25.2 to 7.28.1

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

#498 - Bump snakemake from 7.25.2 to 7.26.0

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

#497 - Bump snakemake from 7.25.2 to 7.25.4

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

#496 - Bump snakemake from 7.25.2 to 7.25.3

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

#495 - Bump snakemake from 7.25.0 to 7.25.2

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

#494 - 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

#493 - 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

#492 - 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

#491 - Bump snakemake from 7.21.0 to 7.24.0

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

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

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

#489 - Bump snakemake from 7.21.0 to 7.23.1

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

#488 - Bump snakemake from 7.21.0 to 7.22.0

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

#487 - Bump snakemake from 7.20.0 to 7.21.0

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

#486 - 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

#485 - What should we benchmark?

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

#484 - Bump snakemake from 7.19.0 to 7.19.1

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

#483 - Bump snakemake from 7.18.2 to 7.19.0

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

#482 - Bump actions/cache from 2 to 3

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

#481 - [MRG] update actions to use mambaforge and caching, too

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

#480 - [MRG] add pip check to github actions

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

#479 - [MRG] update versions of sourmash, screed, and snakemake

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

#478 - [MRG] update when GitHub actions run: on PRs, on merge to latest, and daily

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

#476 - Bump snakemake from 7.3.8 to 7.18.2

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

#475 - Bump codecov/codecov-action from 1 to 3

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

#474 - Bump actions/checkout from 2 to 3

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

#473 - Bump actions/setup-python from 2 to 4

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

#472 - [MRG] enable dependabot

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

#471 - AttributeError: 'str' object has no attribute 'name'

Issue - State: closed - Opened by maureenbug about 2 years ago - 7 comments

#470 - look into GGCAT for compaction

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

#469 - is it time for spacegraphcats v3?

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

#468 - [MRG] add fixes in #294 to the right branch

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

#467 - Snakemake error when building catlas

Issue - State: open - Opened by christygrettenberger about 2 years ago - 6 comments

#466 - [MRG] update sourmash req to 4.5.0

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

#465 - are neighborhoods shell-like?

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

#463 - does protein query support degenerative amino acid alphabets?

Issue - State: open - Opened by taylorreiter over 2 years ago - 2 comments

#459 - [MRG] add `mamba` as a conda dependency, b/c snakemake wants it.

Pull Request - State: closed - Opened by ctb over 2 years ago - 1 comment

#458 - add mamba as a dependency?

Issue - State: closed - Opened by taylorreiter over 2 years ago

#457 - experiment with AGC for fast retrieval of unitigs

Issue - State: open - Opened by ctb over 2 years ago - 1 comment

#455 - snakemake errors when running sgc

Issue - State: open - Opened by dnolin13 almost 3 years ago - 3 comments

#454 - [WIP] switch protein annotation stuff over to sqlite, for memory

Pull Request - State: open - Opened by ctb almost 3 years ago - 3 comments

#452 - integrate gather-style approach directly into spacegraphcats?

Issue - State: open - Opened by ctb almost 3 years ago - 7 comments

#451 - should we add abundance counting into config file?

Issue - State: open - Opened by ctb almost 3 years ago - 3 comments

#450 - explore bcalm max-memory parameter

Issue - State: open - Opened by ctb about 3 years ago

#449 - [WIP] implement 'gather'-style behavior to choose the best set of protein matches for nodes

Pull Request - State: open - Opened by ctb about 3 years ago - 12 comments

#448 - annotating graphs with proteins, round 2

Issue - State: open - Opened by ctb about 3 years ago - 4 comments

#447 - AssertionError spacegraphcats.cdbg.index_reads on branch `prot_search`

Issue - State: closed - Opened by taylorreiter about 3 years ago - 12 comments

#446 - get allele seqs (and/or SNPs) from sgc GFA file?

Issue - State: open - Opened by maureenbug about 3 years ago - 3 comments

#444 - [MRG] add translated catlas annotation functionality w/multifasta approach

Pull Request - State: closed - Opened by ctb about 3 years ago - 5 comments

#443 - [MRG] better integrate protein search of unitigs into spacegraphcats

Pull Request - State: closed - Opened by ctb about 3 years ago - 1 comment

#442 - [MRG] clean up some unused code in index_cdbg_by_multifasta.py

Pull Request - State: closed - Opened by ctb about 3 years ago - 1 comment

#440 - Documentation of the file headers in the catlas output

Issue - State: open - Opened by drtamermansour about 3 years ago - 3 comments
Labels: documentation

#439 - notes on using the spacegraphcats catlas structure

Issue - State: open - Opened by ctb about 3 years ago - 1 comment
Labels: documentation

#438 - [MRG] close databases and files appropriately

Pull Request - State: closed - Opened by ctb about 3 years ago - 2 comments

#437 - thoughts about annotating a cDBG with protein queries

Issue - State: closed - Opened by taylorreiter about 3 years ago - 7 comments

#435 - Using spacegraphcats for kmer partitioning.

Issue - State: open - Opened by drtamermansour about 3 years ago - 3 comments

#434 - Error in rule index_reads: `sqlite3.OperationalError: database or disk is full`

Issue - State: closed - Opened by taylorreiter about 3 years ago - 5 comments
Labels: error message

#433 - note on paired-end foo

Issue - State: open - Opened by ctb about 3 years ago

#432 - [MRG] remove unnecessary bcalm_unitigs cli arg

Pull Request - State: closed - Opened by ctb over 3 years ago

#431 - [MRG] switch 'master' refs over to 'latest' in docs

Pull Request - State: closed - Opened by ctb over 3 years ago - 1 comment

#430 - [WIP] add GFA parsing scripts and explore working with bifrost

Pull Request - State: open - Opened by ctb over 3 years ago - 3 comments

#429 - [WIP] change k-mer hashing to use sourmash hash function

Pull Request - State: open - Opened by ctb over 3 years ago - 5 comments

#428 - Annotating the catlas

Issue - State: open - Opened by taylorreiter over 3 years ago - 1 comment
Labels: Results

#427 - investigate 'cuttlefish' for cDBG construction

Issue - State: open - Opened by ctb over 3 years ago

#425 - is there a way to extract reads by dominator id?

Issue - State: open - Opened by taylorreiter over 3 years ago

#424 - Fix sanity check in rdomset.domination_graph()

Pull Request - State: closed - Opened by mogproject over 3 years ago - 1 comment

#423 - Sanity check in rdomset.domination_graph not working

Issue - State: closed - Opened by mogproject over 3 years ago - 3 comments

#422 - [MRG] add cdbg node annotations to multifasta query output

Pull Request - State: closed - Opened by taylorreiter over 3 years ago - 1 comment

#421 - catlas viz idea with dom diff abund application

Issue - State: open - Opened by taylorreiter over 3 years ago - 1 comment

#419 - [ MRG] fix command typo in documentation

Pull Request - State: closed - Opened by taylorreiter over 3 years ago

#417 - fragmented graph results only under certain conditions??

Issue - State: open - Opened by maureenbug over 3 years ago - 12 comments