CHANGELOG.md

Change Log

All notable changes to the docker-bio-linux8-resolwe project will be documented in this file. This project adheres to Semantic Versioning.

Unreleased

Added

• Script serving as container's entrypoint executable that enables dynamically setting user and group IDs of the user running in the container by passing them via environment variables.
• Documentation on using the image, including mounting a local directory inside the container and passing the host user's user and group IDs to the container via environment variables.
• gosu 1.9.
• scikit-learn 0.14.1.
• PyPy 2.2.1.
• HTSeq 0.6.1p1.
• pysam 0.9.1.4.
• xlrd (currently, 0.9.2).
• Utility scripts from SortMeRNA package.

Changed

• No longer set WORKDIR to /home/biolinux/data.
• Update Resolwe Runtime Utilities to 1.1.0.

Removed

• Remove creation of ~/auxiliary_data directory since it is no longer necessary.
• Remove creation of ~/data and ~/upload directories since they will get automatically created when volumes are mounted from the host.

0.2.0 - 2016-05-17

Added

• Script that calculates the change in size between the base and the new Docker image
• JBrowse 1.12.0.
• BEDOPS 2.4.15.
• GenomeTools 1.5.3.
• tabix (currently, 0.2.6).
• bedtools (currently, 2.17.0).
• p7zip-full (currently, 9.20.1).
• bamliquidator 1.2.0-0ppa1~trusty.
• MACS2 2.1.1.20160309.
• ROSE2 1.0.2.
• R packages:
  • argparse
  • chemut
  • devtools
  • RNASeqT
• Bioconductor R packages:
  • Rsamtools
  • reshape2
  • seqinr
  • stringr
  • tidyr
• vcfutils.pl from samtools package.
• cutadapt 1.9.1.
• HISAT2 2.0.3-beta.

0.1.0 - 2016-02-04

• Initial release.