Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
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
#398 - Propagation `make clean` – use `xargs` instead of `-exec` with find
Issue -
State: open - Opened by karel-brinda 7 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
#355 - When the number of input files is large, prophyle index check is too slow
Issue -
State: open - 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
#319 - Cluster sync lantencies => prophyle_propagation_postprocessing.py: FileNotFoundError: [Errno 2] No such file or directory
Issue -
State: open - Opened by karel-brinda over 6 years ago
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