Biorunner is a way to quickly install a controlled set of tools widely used in Life Sciences and Bioinformatics. For researchers, installing all tools manually can be challanging; with this collection, you have one chorerent set of all tools, with known versions, in a single image file.
Although developed for use on high-performance compute clusters in supercomputing centres, you can install the tools on a local workstation or even on your own computer, to have exactly the same environment locally as on the supercomputing centre.
Biorunner uses Singularity [1] for packaging all applications in a single image, and also needs it where running the applications. Installing Biorunner involves putting the image your PATH environment, adding a wrapper script that runs commands inside a Singularity container, and symbolic links for all commands availble in the Biorunner image, pointing to the wrapper script.
For building your own image, you need, on the system where you are building the image:
- singularity; version 3 or later
- root access
- at least 5 Gigabytes of free disk space
- a good network connection
Now, become root; as root
-
first, set the environment variable SINGULARITY_TMPDIR to a path where you have at least 5 GB of free disk space.
If you do not set this variable, singularity will use ''/var/tmp''.
To set it to, for example, a directory called "/scratch", do """ export SINGULARITY_TMPDIR=/scratch """
-
Do """ singularity build biorunner-2019b.sif biorunner.def """
That is it! This may take a while, but after the build, you have a container image file "biorunner-2019b.sif". See INSTALLATION for further installation instructions.
Thefollowing applications are exposed through Biorunner:
- bowtie2
- samtools
- ncbi-blast2
- minimap
- miniasm
- fastqc
- poretools
- clustal Omega
- clustal x
- SPAdes
- Deepbinner
- Nanopolish
- trimAl
- Filtlong
- Racon
- minimap2
- Pilon
- Unicycler
- Mauve
- PhyML, SMS-PhyML
- Centrifuge
- Hmmer
- Prokka (v1.14.6)
- nanopack
|-----------------------------|--------------|
Package | Version |
---|---|
SMS-PhyML | 1.8.4 |
Prokka | 1.14.6 |