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