chanzuckerberg / shasta-docker Goto Github PK

This project is abandoned.

Please refer to the Shasta repo fork for software release options.

Docker images for doing de-novo assembly using Shasta.

Docker can be installed on most platforms. Detailed instructions available at https://docs.docker.com/engine/install/

https://docs.docker.com/engine/install/linux-postinstall/#manage-docker-as-a-non-root-user

Shasta Docker images are available for the x86_64 (amd64) & arm64v8 (aarch64) platforms.

You can use the following command to see which Shasta releases are available and how to use them.

docker run ghcr.io/chanzuckerberg/shasta:latest --help

OR

docker run ghcr.io/chanzuckerberg/shasta-arm64v8:latest --help

The following examples assume that you're on the x86_64 (amd64) platform. If you're on the arm64v8 (aarch64) platform, replace ghcr.io/chanzuckerberg/shasta:latest with ghcr.io/chanzuckerberg/shasta-arm64v8:latest, in the following examples.

1. If the reads (fasta/fastq) files are located at /path/to/folder/containing/reads and you would like the Assembly Directory be created in the current working directory, then

docker run -u `id -u`:`id -g` \
    -v `pwd`:/output \
    -v /path/to/folder/containing/reads:/reads:ro \
    ghcr.io/chanzuckerberg/shasta:latest \
    <SHASTA-VERSION-STRING> \
    --input /reads/input.fasta

2. If you would also like to provide a Shasta conf file, located in the current working directory, then

docker run -u `id -u`:`id -g` \
    -v `pwd`:/output \
    -v /path/to/folder/containing/reads:/reads:ro \
    ghcr.io/chanzuckerberg/shasta:latest \
    <SHASTA-VERSION-STRING> \
    --input /reads/input.fasta \
    --conf Nanopore-Sep2020.conf

3. If you would also like to override specific configuration parameters, then

docker run -u `id -u`:`id -g` \
    -v `pwd`:/output \
    -v /path/to/folder/containing/reads:/reads:ro \
    ghcr.io/chanzuckerberg/shasta:latest \
    <SHASTA-VERSION-STRING> \
    --input /reads/input.fasta \
    --conf Nanopore-Sep2020.conf \
    --MinHash.minBucketSize 13 \
    --assemblyDirectory ShastaRunInDocker

Passing the user:group of the user running the Docker command with the -u flag will result in the Assembly Directory being owned by that user. Otherwise, the Assembly Directory will be owned by root.

Detailed information about running a Shasta assembly can be found at https://chanzuckerberg.github.io/shasta/Running.html.

Optimal Shasta performance can be achieved by using --memoryMode filesystem --memoryBacking 2M. However, this requires the --privileged flag, as shown below

docker run --privileged \
    -v `pwd`:/output \
    ghcr.io/chanzuckerberg/shasta:latest \
    <SHASTA-VERSION-STRING> \
    --input input.fasta --memoryMode filesystem --memoryBacking 2M