bionitio-team/bionitio

Issues

• Add .gitignore files

  #79 opened 4 years ago by ewels
  0

• Set repos up as GitHub Template repos

  #78 opened 4 years ago by ewels
  1

• Python - setuptools

  #31 opened 8 years ago by happykhan
  3

• Consider using GitHub actions instead of Travis

  #77 opened 4 years ago by bjpop
  1

• Document generation for Sphinx

  #76 opened 4 years ago by bjpop
  0

• GitHub API is deprecating password access. Use personal access token instead (PAT).

  #75 opened 5 years ago by bjpop
  0

• Consider mounting functional_tests directory in Docker, rather than including it in the containers

  #74 opened 5 years ago by bjpop
  0

• Test GitHub integration on Windows

  #73 opened 6 years ago by bjpop
  0

• Underscore in NAME clashes with R package syntax

  #47 opened 6 years ago by lonsbio
  5

• bionitio.pl only runs with the .pl extension

  #64 opened 6 years ago by AnnaSyme
  2

• Invalid fasta file behaviour

  #62 opened 7 years ago by multimeric
  0

• perl version generates warnings/errors on single_greather_than.fasta

  #44 opened 6 years ago by bjpop
  1

• Standardise prompt icon

  #63 opened 6 years ago by multimeric
  1

• Looks similar to cookie-cutter

  #68 opened 6 years ago by lachlansimpson
  2

• Consistent error handling

  #12 opened 6 years ago by bjpop
  2

• URL in setup.py points to bjpop GitHub

  #69 opened 6 years ago by hdashnow
  1

• Missing expected file still passes

  #70 opened 6 years ago by trickytank
  0

• bootstrap script should respond better to github errors

  #66 opened 6 years ago by bjpop
  1

• Create placeholder for license name, similar to BIONITIO_AUTHOR

  #67 opened 6 years ago by bjpop
  1

• bionitio perl5 and ruby need a licence file

  #65 opened 6 years ago by AnnaSyme
  2

• Docker container

  #41 opened 6 years ago by bjpop
  1

• boot.sh fails if name contains bionitio

  #59 opened 7 years ago by lonsbio
  1

• Consider making installation instructions for each language more detailed

  #53 opened 7 years ago by AnnaSyme
  1

• Functional tests missing with `git clone`

  #61 opened 7 years ago by lonsbio
  1

• README for new bootstrapped projects contains bad travis URL

  #58 opened 7 years ago by bjpop
  2

• Use -g info to project name plus `-team` rather than user or local

  #60 opened 7 years ago by lonsbio
  1

• Consider making github and travis instructions more detailed

  #54 opened 7 years ago by AnnaSyme
  1

• Overview page: clarify tool use vs template tool setup

  #55 opened 7 years ago by AnnaSyme
  2

• boostrap script should remove the readme_includes directory in newly created projects

  #56 opened 7 years ago by bjpop
  1

• Make all implementations call their executable binitio (and remove any extensions in the name)

  #57 opened 7 years ago by bjpop
  0

• What is the intended semantics of the verbose flag?

  #5 opened 7 years ago by bjpop
  3

• Can we add some logging to the program?

  #9 opened 7 years ago by bjpop
  3

• Version of python in travis.yml - multiple?

  #49 opened 7 years ago by AnnaSyme
  1

• Restructure repository by splitting into separate repos

  #51 opened 7 years ago by multimeric
  8

• biotool-js : failing on empty file test

  #34 opened 7 years ago by drpowell
  2

• Typo in file name (within test_data)

  #48 opened 7 years ago by AnnaSyme
  1

• Point to location of bionitio-boot.sh in README

  #50 opened 7 years ago by claresloggett
  1

• Check that renaming directories and files in biotool-boot.sh is safe and does not clash with existing names

  #46 opened 8 years ago by bjpop
  1

• Perl program uses /dev/stdin to read from stdin, I'm not sure that this is portable

  #45 opened 8 years ago by bjpop
  2

• biotool-c not handling empty file correctly

  #33 opened 8 years ago by tseemann
  1

• biotool-java failing on empty file test

  #35 opened 8 years ago by drpowell
  1

• Handling of a dodgy file when multiple files supplied

  #32 opened 8 years ago by tseemann
  2

• Make it more useful

  #38 opened 8 years ago by Slugger70
  2

• biotool-R failing tests

  #37 opened 8 years ago by drpowell
  0

• Rounding differences in languages when computing average sequence length

  #4 opened 8 years ago by bjpop
  2

• biotool-cpp doesn't handle empty file

  #36 opened 8 years ago by drpowell
  2

• JS does not return correct exit status on command line error

  #25 opened 8 years ago by bjpop
  2

• Consistent handling of empty files

  #7 opened 8 years ago by drpowell
  1

• Bug in Perl code (and perhaps others): minlen can cause the program to claim input file is not FASTA if there are 0 reads greater than the minimum length

  #13 opened 8 years ago by bjpop
  1

• README.md wrong?

  #11 opened 9 years ago by drpowell
  2