BioVM 18.04.1

Summary of changes in BioVM 18.04.1 — a Linux virtual machine based on Ubuntu for teaching and learning Bioinformatics.

Note: BioVM is now Biomint.

The following changes are implemented in this release:

bioenv is now an empty Conda environment

In the previous release, the following software were pre-installed in bioenv (the default conda environment) — bedtools, blast, bowtie2, bwa, clustalo, cutadapt, fastqc, fastx_toolkit, mummer, muscle, primer3, samtools and trimmomatic. As it is hard to decide on a default list of software, this configuration is now modified so users can choose the software they would like to install.

After activating bioenv, the conda install command can be used to install new software, for example:

ca bioenv
conda install blast

ca is just an alias to
conda /home/biovm/Programs/miniconda3/bin/activate

Also, links to conda activate and deactivate commands have now been removed from ~/Programs/bin directory as this leads to conflicts with Python virtualenv creation.

R 3.4 and RStudio update

R 3.4 has been updated to the latest stable version available from CRAN (3.4.4). The Cran2Deb4Ubuntu PPA has now been added to the system.

This provides some additional binary packages for R (4,000+).

RStudio has been updated to version 1.2.5033. The editor’s font size has been increased (view.zoomLevel=1.2)

System configuration changes

The following system libraries are now included — curl, jpeg, png, setuptools, xml2, and freetype. This will be useful for compiling software requiring these libraries.

The virtual machine’s 3D acceleration is now disabled as this configuration will not be supported in newer VirtualBox releases.

Blog post updates:

  • Oct 6, 2023: Remove broken links.