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Tool: BioVM - a virtual machine for Bioinformatics

Hi all,

I would like announce the availability of BioVM - a virtual machine for Bioinformatics.

These are the main features

  • A minimal installation of Ubuntu Linux (MATE, 16.04 LTS).
  • Pre-installed software - Bedtools, Bowtie 2, BWA, ClustalO, Cutadapt, EMBOSS (with the Jemboss and Emboss Explorer graphical user interfaces and the EMBASSY packages), FastQC, FASTX-Toolkit, Mummer, Muscle, NCBI BLAST+, Primer 3, Samtools, Tophat, TreeviewX, Trimmomatic, UGENE.
  • A local instance of Galaxy - the open web-based platform for computational biomedical research.
  • The Conda package manager with a default environment setup. Conda is used to install packages (with dependencies) written in languages like Python, R, Ruby, Lua, Scala, Java, C/C++ and Fortran.
  • Docker installed and ready to use.
  • Programming and system tools installed, support for Python, PERL and R.

BioVM desktop - the Bioinformatics category in the menu

Getting started

You will need to have VirtualBox installed. BioVM itself does not require installation. You can download the appliance from the website, import and the launch the virtual machine from VirtualBox.

Please visit the website to learn more about the project and to download the appliance.

BioVM is an Open Source project released under the GPL v3 license. It is built using Vagrant, Ansible and VirtualBox. Source code is available on Github.

Would love to hear your feedback!

linux virtual machine ubuntu galaxy conda tool
• 439 views • link
written by vimalkvn vimalkvn

:)

• 0 views • link
written by andrew.j.skelton73 andrew.j.skelton73

Thanks for that. The version of TopHat included is 2.1.0. I see the note also on the website. Will remove it in the next release and consider including HISAT2 instead.

• 0 views • link
written by vimalkvn vimalkvn

Without wishing to sound too negative, what does this do that BioLinux doesn't already?

• 0 views • link
written by Joe Joe

The main advantages are

1. Increased software availability

  • Conda enables the installation and usage of software that is not yet available in the repositories. For example, HISAT2 is not available in the package repositories for Ubuntu 16.04. Here is a demo of using Conda to install the latest version of HISAT2 in BioVM. (Thanks to Bioconda and conda-forge).

    Asciicast: Using Conda to install a program that is not available in the repositories

  • New packages from the Ubuntu/Debian repositories that were made available for Ubuntu 16.04 which BioVM is based upon. For example Kraken was not available on 14.04 but is available from 16.04 onwards (Thanks to Debian Med).

  • It is possible to use software available as Docker images. For example, VirSorter.
  • Similarly packages from CPAN, CRAN and PyPI can be installed easily without admin privileges using cpanm, install.packages/biocLite and virtualenv/pip respectively.

2. Support for programming in Python (IPython3, Jupyter notebook, PyCharm IDE) and R (RStudio).

3. BioVM is modular Components in BioVM are defined as Ansible roles and the VM is built using Vagrant. For example, the galaxy role installs PostgreSQL, Apache + modules, creates a database, downloads and configures Galaxy. New roles can be defined or existing ones removed to create a customised version of the VM.

The only limitation currently is that some packages will need to be updated manually - Conda, Galaxy and RStudio.

• 0 views • link
written by vimalkvn vimalkvn

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