bionitio-team / bionitio

Demonstrating best practices for bioinformatics command line tools

bionitio-team/bionitio Issues

Add .gitignore files
Updated 4 years ago
Set repos up as GitHub Template repos
Updated 4 years ago1
Python - setuptools
Updated 4 years ago3
Consider using GitHub actions instead of Travis
Updated 4 years ago1
Document generation for Sphinx
Updated 4 years ago
GitHub API is deprecating password access. Use personal access token instead (PAT).
Updated 5 years ago
Consider mounting functional_tests directory in Docker, rather than including it in the containers
Updated 5 years ago
Test GitHub integration on Windows
Updated 5 years ago
Underscore in NAME clashes with R package syntax
Closed 5 years ago5
bionitio.pl only runs with the .pl extension
Closed 6 years ago2
Invalid fasta file behaviour
Updated 6 years ago
perl version generates warnings/errors on single_greather_than.fasta
Closed 6 years ago1
Standardise prompt icon
Closed 6 years ago1
Looks similar to cookie-cutter
Closed 6 years ago2
Consistent error handling
Closed 6 years ago2
URL in setup.py points to bjpop GitHub
Closed 6 years ago1
Missing expected file still passes
Updated 6 years ago
bootstrap script should respond better to github errors
Closed 6 years ago1
Create placeholder for license name, similar to BIONITIO_AUTHOR
Closed 6 years ago1
bionitio perl5 and ruby need a licence file
Closed 6 years ago2
Docker container
Closed 6 years ago1
boot.sh fails if name contains bionitio
Closed 7 years ago1
Consider making installation instructions for each language more detailed
Closed 7 years ago1
Functional tests missing with `git clone`
Closed 7 years ago1
README for new bootstrapped projects contains bad travis URL
Closed 7 years ago2
Use -g info to project name plus `-team` rather than user or local
Closed 7 years ago1
Consider making github and travis instructions more detailed
Closed 7 years ago1
Overview page: clarify tool use vs template tool setup
Closed 7 years ago2
boostrap script should remove the readme_includes directory in newly created projects
Closed 7 years ago1
Make all implementations call their executable binitio (and remove any extensions in the name)
Updated 7 years ago
What is the intended semantics of the verbose flag?
Closed 7 years ago3
Can we add some logging to the program?
Closed 7 years ago3
Version of python in travis.yml - multiple?
Closed 7 years ago1
Restructure repository by splitting into separate repos
Closed 7 years ago8
biotool-js : failing on empty file test
Closed 7 years ago2
Typo in file name (within test_data)
Closed 7 years ago1
Point to location of bionitio-boot.sh in README
Closed 7 years ago1
Check that renaming directories and files in biotool-boot.sh is safe and does not clash with existing names
Closed 8 years ago1
Perl program uses /dev/stdin to read from stdin, I'm not sure that this is portable
Closed 8 years ago2
biotool-c not handling empty file correctly
Closed 8 years ago1
biotool-java failing on empty file test
Closed 8 years ago1
Handling of a dodgy file when multiple files supplied
Closed 8 years ago2
Make it more useful
Closed 8 years ago2
biotool-R failing tests
Closed 8 years ago
Rounding differences in languages when computing average sequence length
Closed 8 years ago2
biotool-cpp doesn't handle empty file
Closed 8 years ago2
JS does not return correct exit status on command line error
Closed 8 years ago2
Consistent handling of empty files
Closed 8 years ago1
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
Closed 8 years ago1
README.md wrong?
Closed 8 years ago2