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