A new release of BioVM with updated software, Galaxy configuration, documentation and includes recommendations for installing new software.
Note: BioVM is now Biomint.
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:
The command to activate bioenv is
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:
Disabled autostart of Galaxy with supervisor at VM start. This can be changed in
Added Python 2 and Python 3 headers, library and development tools.
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.
- 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
Blog post updates:
Oct 2, 2023: Remove link to documentation (broken).