A new release of BioVM is now available for download.

What's new

Latest bioinformatics software

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

Note

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

Activate environment ca env_name

Deactivate environment ce

Previously, these were st and dt respectively.

Galaxy - Docker support, simple commands for management

  • The docker support is added in the job configuration.
  • Galaxy can now be managed using these simple commands (aliases) - start-galaxy, stop-galaxy and restart-galaxy.
  • Galaxy does not start automatically when the VM boots. This can be changed in /etc/supervisor/conf.d/galaxy.conf (autostart = true)

Updated documentation

https://biovm.readthedocs.io.

Recommendations for installing new software in BioVM

Documentation includes an infographic with recommended steps for installing new software

A support forum has also been setup Join the community on Spectrum

Minor changes

  • Added Python (2 & 3) headers, library and development tools.
  • Removed command-not-found program and TopHat.
  • Updated RStudio (1.1.419 -> 1.1.442).
  • Vagrant
    • Changed minimum memory requirement from 2 to 4GB.
    • Switched on verbose flag.
    • Disabled vagrant box update check to speed up builds.
  • Desktop
    • Font files are now included in the Github repository.
    • Increased panel size, disabled panel animations.