Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of https://github.com/clinical-genomics/mutacc

https://github.com/clinical-genomics/mutacc - Fixed Picard version in Dockerfile

[1.7.2]

Fixed

  • Picard version in Dockerfile to be 3.1.0

- Python
Published by northwestwitch over 2 years ago

https://github.com/clinical-genomics/mutacc - Fixed Docker build and push action

[1.7.1]

Fixed

  • workflow step version in docker_build_n_publish GitHub action

- Python
Published by northwestwitch over 2 years ago

https://github.com/clinical-genomics/mutacc - Removed deprecated code, unfreezed pymongo lib and Python 3.11 in Dockerfile

[1.7]

Added

  • Integration test with MongoDB v7 ### Changed
  • Moved tests and coverage from Travis to GitHub actions
  • Updated python version and versions of some GitHub actions
  • Unfreeze cyvcf2 lib to be able to install the software with Python>=3.8
  • Installation instructions on README page to install mutacc using Python 3.8
  • Unfreeze pymongo requirement and removed deprecated pymongo code to support latest version of MongoDB
  • Updated pythin version to 3.11 in Dockerfile
  • Updated MongoDB version to 7 in docker-compose.yml file ### Fixed
  • Badge on Readme page
  • GitHub action to push the right image to Docker Hub
  • Replaced deprecated pkg_resources lib with importlib_resources
  • Path to app in testsandcoverage.yml, coveralls step

- Python
Published by northwestwitch over 2 years ago

https://github.com/clinical-genomics/mutacc - Freeze PyMongo to version<4.0

[1.6.3]

Fixed

  • Freeze PyMongo to version<4.0

- Python
Published by northwestwitch over 2 years ago

https://github.com/clinical-genomics/mutacc - New token name used by PyPI push action

[1.6.2]

Fixed

  • Token name used by PyPI push action once again

- Python
Published by northwestwitch over 4 years ago

https://github.com/clinical-genomics/mutacc - Fixed token name used by PyPI push action

[1.6.1]

Fixed

  • Token name used by PyPI push action

- Python
Published by northwestwitch over 4 years ago

https://github.com/clinical-genomics/mutacc - Fix mongo-adapter and PyYAML dependency issues. Improved Dockerfile

[1.6]

Changed

  • Build and use local Dockerfile when creating demo container in docker-compose
  • Minify Docker image by adding a multi-stage build and manually installing Picard and the Java Virtual Machine
  • Speed up Docker image building by basing it on another image with cyvcf2 already installed ### Fixed
  • Parse yaml config files using yaml.safe_load to avoid missing Loader error due to deprecation introduced by PyYAML 6.0
  • Typo in docker-compose file
  • Fix mongo-adapter dependency to use version>=0.3.3. Previous versions have a way too short connection timeout and approximate URI log print

- Python
Published by northwestwitch over 4 years ago

https://github.com/clinical-genomics/mutacc - Improved docker file, new GitHub Actions and support for MongoDB connection URIs

[1.5]

Added

  • A docker-compose file that loads demo data on a MongoDB instance and exports results to the current directory of the user
  • GitHub action building a repo image and pushing it to Docker Hub when a new release is published
  • A command line option to allow mongo URI connections (already supported from config file)
  • GitHub action building the software and publishing it to PyPI when a new release is published ### Changed
  • Dockerfile now based on a miniconda3 image with commands runned as a non-root user

- Python
Published by northwestwitch almost 5 years ago