BioVM 18.04

A new release of BioVM is now available for download.

What’s new

Includes latest software, updates to Galaxy configuration, updated documentation and recommendations for installing new software.

Latest bioinformatics 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: st → ca and dt → ce.

The command to activate bioenv is ca bioenv.

Galaxy configured to support Docker and commands provided for management

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
/etc/supervisor/conf.d/galaxy.conf.

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

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