BioVM is an Ubuntu Linux Virtual Machine for Teaching and Learning Bioinformatics. A new release is now available for download.
Virtual machine image from SourceForge (OVA format).
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
Also, links to conda
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¶
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 (
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.