Initial version from: https://github.com/srivathsapv/wga-essentials
This docker image contains essential packages and tools for whole genome assembly and alignment. The following are the packages that are available in this docker image:
- fastqc
- jellyfish
- spades
- mummer
- samtools
- freebayes
- bcftools
- bowtie2
Follow the below links to install Docker on various operating systems
The below steps worked on MacBook Pro (OS X High Sierra)
$ docker pull mschatz/wga-essentials
$ docker run -it -d -v <source_code_path>:/root/<source_code> mschatz/wga-essentials bin/bash
Note: The <source_code_path> can be your working directory in your host machine (local machine) and <source_code> will be the mountpoint inside the container. This enables the docker container to access your local files (code and reads/reference genome files)
Note 2: On a recent Mac with a M1 or later chip you will need to specify the kernel, e.g.
$ docker run --platform linux/amd64 -it -d -v asm:/root/asm mschatz/wga-essentials bin/bash
The above command will print a long hexadecimal string. Ex:
50c27954340f691c1e63655302a58349d48018b1610b8fe0092ba94a07e5914a
Take the first 6 characters of this string and execute
$ docker exec -it 50c279 bin/bash
This will take you to the bash of the docker container. To go inside the source code folder execute
# cd /root/source_code
Assume you have a ref.fa file in your source_code folder. Then run the following command
# samtools faidx ref.fa
If this command executes successfully, it means your setup process is complete.
Acknowledgement:
Many thanks to phizaz/bioconda from where I took the base images for python3 and miniconda.