A new release of BioVM is now available for download.

What's new

Latest bioinformatics software

Conda is now used for most bioinformatics software. An environment called bioenv is setup with latest available versions of bedtools, blast, bowtie2, bwa, clustalo, cutadapt, fastqc, fastx_toolkit, mummer, muscle, primer3, samtools and trimmomatic.

The aliases (commands) for activating and deactivating
conda environments have been changed:
stca and dtce

The command to activate bioenv is ca bioenv.

Galaxy - Docker support, simple commands for management

Added support for Docker as a destination in job configuration.

Added aliases for managing Galaxy:
start-galaxy, stop-galaxy, restart-galaxy.

Disabled autostart of Galaxy with supervisor at VM start. This can be changed in /etc/supervisor/conf.d/galaxy.conf.

Minor changes

  • Added Python (2 & 3) headers, library and development tools.
  • Removed command-not-found program as it could cause confusion as multiple package managers in use.
  • Removed TopHat. why?
  • Updated RStudio (1.1.419 -> 1.1.442).
  • Vagrantfile changes
    • Changed minimum memory requirement to 4GB from 2GB.
    • Switched on verbose flag.
    • Disabled box update check to speed up builds.
  • Desktop
    • Font files are now included in the repo.
    • Increase panel size, disabled panel animations.

Updated documentation

Available online at https://biovm.gitlab.io.

Recommendations for installing new software in BioVM

Documentation includes an infographic with recommended steps for installing new software