eipm/bioinformatics repository overview

⁠Bioinformatics

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

It includes:

• R 4.0.2
• bedtools (installed from distro with apt install: current version 2.27.1)
• samtools & htslib 1.8
• bcftools (installed from distro with apt install: current 1.10.2-3 using htslib 1.10.2-3)
• vcftools (installed from distro with apt install: current 0.1.16)
• bwa (installed from distro with apt install: current 0.7.17-r1188)
• pindel (latest:0.2.5b9, 20160729)

The installed tools are the latest available as of Aug 18, 2020.

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

⁠Transform BAM

This image also include an utility called transformBAM.sh that will transform a BAM file by replacing IDs in the header. It will warn if changes need to occur in the content of the BAM file, e.g. the RG group. To use it, simply type transformBAM.sh and the usage will be displayed.