Bioinformatics

This application provides some of the basic bioinformatics tools for development, debugging, and troubleshooting applications.

It includes:

• R 4.2.2
• bedtools (installed from distro with apt install: current version v2.30.0)
• bcftools (installed from distro with apt install: current 1.13 (using htslib 1.13+ds)
• vcftools (installed from distro with apt install: current 0.1.16)
• bwa (installed from distro with apt install: current 0.7.17-r1188)
• samtools (1.19 (using htslib 1.19))
• pindel (latest:0.2.5b9, 20160729)
• STAR (2.7.6a)

Note: pindel includes a fix from a non-merged branch (see Dockerfile).

Common R packages are also installed. See installPackages.R to see which ones.

Installation

To install the component for docker hub (assumining version 1.0.0):

docker pull eipm/bioinformatics:1.0.0

The user must have successfully logged in the docker DTR with docker login

Usage

The basic way to use this component is:

docker run --rm -it --name bioinfo -u $(id -u):$(id -g) eipm/bioinformatics:1.0.0  /bin/bash

If specific file mounts are needed, use the -v option (see docker run reference documentation). For example:

docker run --rm -it --name bioinfo -u $(id -u):$(id -g) -v /path/to/local/folder/:/path/to/internal/folder eipm/bioinformatics:1.0.0  /bin/bash

Tip: use the :ro option to mount read-only folders, e.g. -v /path/to/local/folder/:/path/to/internal/folder:ro

Combine pindel VCFs

This utility combine_pindel_vcfs.sh takes multiple pindel results and merge them [TBDs]