Ecosyste.ms: Issues

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GitHub / prophyle/prophyle issues and pull requests

#405 - Scheduled monthly dependency update for September

Pull Request - State: open - Opened by pyup-bot 30 days ago

#404 - Scheduled monthly dependency update for August

Pull Request - State: closed - Opened by pyup-bot 2 months ago - 1 comment

#403 - Scheduled monthly dependency update for July

Pull Request - State: closed - Opened by pyup-bot 3 months ago

#402 - Scheduled monthly dependency update for June

Pull Request - State: closed - Opened by pyup-bot 4 months ago

#401 - Scheduled monthly dependency update for May

Pull Request - State: closed - Opened by pyup-bot 5 months ago - 1 comment

#400 - Fix compilation for M1

Pull Request - State: closed - Opened by karel-brinda 5 months ago

#399 - Scheduled monthly dependency update for April

Pull Request - State: closed - Opened by pyup-bot 6 months ago

#397 - Scheduled monthly dependency update for February

Pull Request - State: closed - Opened by pyup-bot 8 months ago

#396 - Scheduled monthly dependency update for January

Pull Request - State: closed - Opened by pyup-bot 9 months ago - 1 comment

#395 - Verify ProPhyle bioconda dependencies

Issue - State: open - Opened by karel-brinda 10 months ago

#394 - Scheduled monthly dependency update for December

Pull Request - State: closed - Opened by pyup-bot 10 months ago

#393 - Scheduled monthly dependency update for November

Pull Request - State: closed - Opened by pyup-bot 11 months ago

#392 - Scheduled monthly dependency update for October

Pull Request - State: closed - Opened by pyup-bot almost 1 year ago

#391 - Scheduled monthly dependency update for September

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

#390 - Scheduled monthly dependency update for August

Pull Request - State: closed - Opened by pyup-bot about 1 year ago - 1 comment

#389 - Scheduled monthly dependency update for July

Pull Request - State: closed - Opened by pyup-bot over 1 year ago - 1 comment

#388 - Scheduled monthly dependency update for June

Pull Request - State: closed - Opened by pyup-bot over 1 year ago - 1 comment

#387 - Scheduled monthly dependency update for May

Pull Request - State: closed - Opened by pyup-bot over 1 year ago - 1 comment

#386 - Scheduled monthly dependency update for April

Pull Request - State: closed - Opened by pyup-bot over 1 year ago

#385 - Scheduled monthly dependency update for March

Pull Request - State: closed - Opened by pyup-bot over 1 year ago - 1 comment

#384 - Scheduled monthly dependency update for January

Pull Request - State: closed - Opened by pyup-bot over 1 year ago - 1 comment

#383 - Bump wheel from 0.37.1 to 0.38.1

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

#382 - Scheduled monthly dependency update for December

Pull Request - State: closed - Opened by pyup-bot almost 2 years ago - 1 comment

#381 - Scheduled monthly dependency update for November

Pull Request - State: closed - Opened by pyup-bot almost 2 years ago - 2 comments

#380 - ProPhyle doesn't work on M1

Issue - State: closed - Opened by karel-brinda almost 2 years ago - 3 comments
Labels: bug, critical

#379 - Scheduled monthly dependency update for October

Pull Request - State: closed - Opened by pyup-bot almost 2 years ago - 1 comment

#378 - Scheduled monthly dependency update for September

Pull Request - State: closed - Opened by pyup-bot about 2 years ago - 1 comment

#377 - Scheduled monthly dependency update for August

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

#376 - Index propagation Makefile cannot deal with spaces in parental dirs

Issue - State: open - Opened by karel-brinda over 2 years ago
Labels: bug, cmd:index

#375 - Scheduled monthly dependency update for May

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

#374 - Scheduled monthly dependency update for March

Pull Request - State: closed - Opened by pyup-bot over 2 years ago - 2 comments

#373 - Scheduled monthly dependency update for January

Pull Request - State: closed - Opened by pyup-bot over 2 years ago - 2 comments

#372 - Scheduled monthly dependency update for December

Pull Request - State: closed - Opened by pyup-bot almost 3 years ago - 2 comments

#371 - Scheduled monthly dependency update for October

Pull Request - State: closed - Opened by pyup-bot almost 3 years ago - 2 comments

#370 - Scheduled weekly dependency update for week 36

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

#369 - Scheduled weekly dependency update for week 35

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

#368 - Scheduled weekly dependency update for week 34

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

#367 - Remove prophyle_index_footprint (redundant)

Issue - State: open - Opened by karel-brinda about 3 years ago

#366 - Use xopen for opening files

Issue - State: open - Opened by karel-brinda about 3 years ago
Labels: enhancement

#365 - Update documentation deployment

Pull Request - State: closed - Opened by karel-brinda about 3 years ago

#364 - update pyup.io config file

Pull Request - State: closed - Opened by karel-brinda about 3 years ago

#363 - Initial Update

Issue - State: closed - Opened by pyup-bot about 3 years ago

#362 - Update codeql

Pull Request - State: closed - Opened by karel-brinda about 3 years ago

#361 - Merge branch 'master' into codeql

Pull Request - State: closed - Opened by karel-brinda about 3 years ago

#360 - Update codecov integration

Pull Request - State: closed - Opened by karel-brinda about 3 years ago

#359 - Enet abundances

Pull Request - State: open - Opened by karel-brinda about 3 years ago

#358 - Replace Travis by Github Actions

Pull Request - State: closed - Opened by karel-brinda about 3 years ago

#357 - Create codeql-analysis.yml

Pull Request - State: closed - Opened by karel-brinda about 3 years ago

#356 - Update Travis configuration

Pull Request - State: closed - Opened by karel-brinda about 3 years ago

#354 - Add the -S param to stop after k-mer propagation

Pull Request - State: closed - Opened by karel-brinda about 3 years ago

#353 - Add a param to stop after k-mer propagation

Issue - State: closed - Opened by karel-brinda about 3 years ago
Labels: feature request

#352 - Fix mimic kraken

Pull Request - State: closed - Opened by karel-brinda about 3 years ago

#351 - ProPhyle 0.3.2.0

Pull Request - State: closed - Opened by karel-brinda about 3 years ago

#350 - Error: /bin/bash: /bin/cat: Argument list too long

Issue - State: closed - Opened by karel-brinda about 3 years ago
Labels: bug

#349 - Arg list

Pull Request - State: closed - Opened by karel-brinda about 3 years ago

#348 - Test output directory

Pull Request - State: closed - Opened by karel-brinda about 3 years ago

#347 - Be robust to ProPhex output truncation

Pull Request - State: closed - Opened by karel-brinda about 3 years ago

#346 - When the tree is too large, propagation progress bar uses too much CPU/IO

Issue - State: closed - Opened by karel-brinda about 3 years ago - 1 comment
Labels: bug, enhancement

#345 - Fix stats in the non-propagation mode

Pull Request - State: open - Opened by karel-brinda about 3 years ago

#344 - Footprint

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

#343 - Automatic autocompletion does weird things with the tree

Issue - State: open - Opened by karel-brinda about 3 years ago - 1 comment
Labels: bug

#342 - Manual compilation of BWA

Issue - State: open - Opened by karel-brinda over 3 years ago - 3 comments
Labels: bug

#341 - If a dataset fully contained, make a single fake sequence of legth 1

Issue - State: open - Opened by karel-brinda almost 4 years ago
Labels: enhancement

#340 - Avoid *

Issue - State: closed - Opened by karel-brinda almost 4 years ago - 1 comment
Labels: bug, duplicate

#339 - Add times to logs in order to simply tuning on clusters

Issue - State: open - Opened by karel-brinda almost 4 years ago
Labels: enhancement

#338 - Allow specifying the number of cores for k-mer propagation

Issue - State: closed - Opened by karel-brinda almost 4 years ago - 1 comment
Labels: enhancement

#337 - RecursionError: maximum recursion depth exceeded while pickling an object

Issue - State: closed - Opened by karel-brinda almost 4 years ago - 1 comment
Labels: bug

#336 - Bump psutil from 5.4.2 to 5.6.6

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago
Labels: dependencies

#335 - Expand IUPAC

Issue - State: closed - Opened by karel-brinda over 4 years ago - 1 comment
Labels: wontfix, feature request

#334 - documentation "7. Analyzing read assignments" is empty

Issue - State: closed - Opened by rchikhi about 5 years ago - 1 comment

#333 - Be robust to ProPhex output truncation

Pull Request - State: closed - Opened by karel-brinda over 5 years ago - 1 comment

#332 - Bacterial library contains archaeal genomes

Issue - State: open - Opened by nataquinones over 5 years ago - 1 comment
Labels: bug, high importance, cmd:download

#331 - When processing of a read fails, add read name to the error message

Issue - State: open - Opened by karel-brinda over 5 years ago
Labels: enhancement

#330 - Don't pass default options to prophex and assignment

Issue - State: open - Opened by karel-brinda over 5 years ago
Labels: enhancement

#329 - Re-running finished decompression damages .bwt

Issue - State: closed - Opened by karel-brinda over 5 years ago
Labels: bug

#328 - prophylelib: shell=True should be avoided

Issue - State: closed - Opened by karel-brinda over 5 years ago - 1 comment
Labels: enhancement, wontfix

#327 - Embed tree into the output bam

Issue - State: open - Opened by karel-brinda over 5 years ago - 1 comment
Labels: feature request

#326 - Bioconda env for prophyle: "CApath: none"

Issue - State: closed - Opened by karel-brinda almost 6 years ago - 1 comment
Labels: bug, invalid

#325 - prophyle-classify: Add a parameter for propagating assignments to the leaf level

Issue - State: open - Opened by karel-brinda about 6 years ago
Labels: feature request, prophyle_assignment

#324 - Unclassified reads are missing from the SAM output

Issue - State: closed - Opened by karel-brinda over 6 years ago
Labels: bug

#323 - Add 'prophyle footprint'

Pull Request - State: closed - Opened by karel-brinda over 6 years ago - 1 comment

#322 - Add `prophyle footprint`

Issue - State: closed - Opened by karel-brinda over 6 years ago
Labels: feature request

#321 - prophyle compress: Add a cli parameter for specifying a tmp dir

Issue - State: open - Opened by karel-brinda over 6 years ago
Labels: enhancement

#320 - prophyle_assignment: not enough values to unpack (expected 2, got 1)

Issue - State: open - Opened by karel-brinda over 6 years ago - 4 comments
Labels: bug

#318 - Index format: add support for multiple klcps

Issue - State: closed - Opened by karel-brinda over 6 years ago
Labels: wontfix, feature request

#317 - Fix a13 travis

Pull Request - State: closed - Opened by simonepignotti over 6 years ago - 1 comment

#316 - Fix tie-lca option

Pull Request - State: closed - Opened by simonepignotti over 6 years ago - 1 comment

#315 - No LCA computation in case of tie

Issue - State: closed - Opened by simonepignotti over 6 years ago
Labels: bug, prophyle_assignment

#314 - Cannot use process substitution as input for prophyle classify

Issue - State: closed - Opened by simonepignotti over 6 years ago - 2 comments
Labels: bug, cmd:classify

#313 - Fix mimic kraken mode

Pull Request - State: closed - Opened by simonepignotti over 6 years ago

#312 - prophyle decompress – "tar: could not chdir to 'database/sparc1_k18'"

Issue - State: closed - Opened by karel-brinda over 6 years ago - 1 comment
Labels: bug

#311 - Parallelize classification

Issue - State: open - Opened by simonepignotti over 6 years ago
Labels: enhancement, cmd:classify

#310 - Mimic kraken mode error

Issue - State: closed - Opened by simonepignotti over 6 years ago - 2 comments
Labels: bug, high importance, prophyle_assignment

#309 - Compute k-mer statistics in non-propagation mode

Issue - State: open - Opened by simonepignotti over 6 years ago
Labels: bug, low importance

#308 - Test A13 – index.fa construction is not unambiguous

Issue - State: closed - Opened by karel-brinda over 6 years ago - 5 comments
Labels: tests

#307 - Add the ln tag (read length)

Pull Request - State: closed - Opened by karel-brinda over 6 years ago

#305 - ProPhyle 0.3.3.0

Pull Request - State: closed - Opened by karel-brinda over 6 years ago - 1 comment