BioVM 18.04

A new release of BioVM with updated software, Galaxy configuration, documentation and includes recommendations for installing new software.

Note: BioVM is now Biomint.

What’s new

Latest software

Conda is now used for the installation of most bioinformatics software. A new environment called bioenv is setup with the latest available versions of Bedtools, BLAST, Bowtie 2, BWA, Clustal O, 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 and commands to start and stop service

The Galaxy job configuration has been updated to support Docker as a job destination.

These command aliases have been added for managing Galaxy:
start-galaxy, stop-galaxy and restart-galaxy.

Disabled autostart of Galaxy with supervisor at VM start. This can be changed in

Minor changes

Added Python 2 and Python 3 headers, library and development tools.

The command-not-found program is removed as it could lead to confusion with multiple package managers in use (apt, snap, conda etc.,).

TopHat has been removed1.

RStudio has been updated from 1.1.419 → 1.1.442.

Vagrantfile changes:

  • The minimum memory requirement has been changed from 4GB to 2GB
  • The verbose flag is now switched on for detailed output during build
  • The vagrant box update check has been disabled to speed up builds

Changes to the desktop configuration:

  • Font files are now included in the repository
  • Panel size has been increased and panel animations are now disabled

Updated documentation

Recommendations for installing new software in BioVM

Blog post updates:

Oct 2, 2023: Remove link to documentation (broken).