Installation instructions for Homebrew missing from documentation

[devin-petersohn]

No description provided.

[devin-petersohn]

@heuermh, are there any other installation methods missing from the docs?

[heuermh]

I suppose we could add bioconda, docker, and singularity if we wanted to. Is this for the README or the proper docs? I want to cut down the README to bare minimum and link to the docs, but that should really go with #1548 which is milestoned 0.24.0.

[devin-petersohn]

This is for the long docs.

[heuermh]

Homebrew:

https://brew.sh/

$ brew tap homebrew/science
$ brew install adam

Linuxbrew:

http://linuxbrew.sh/

$ brew tap homebrew/science
$ brew install adam

Bioconda:

https://bioconda.github.io/#using-bioconda

$ conda config --add channels bioconda
$ conda install adam

Docker image built on linuxbrew:

https://www.docker.com

$ docker run heuermh/adam

Docker image built on bioconda from BioContainers:

https://biocontainers.pro/

$ docker run quay.io/biocontainers/adam

Docker image built for Toil stuff:

(not sure if this is up-to-date)
https://github.com/BD2KGenomics/cgl-docker-lib/blob/master/adam/README.md

$ docker run \
       --net=host \
       -p 9999:9999 \
       quay.io/ucsc_cgl/adam:latest \
       --master spark://<spark_master_ip>:7077 \
       --conf spark.driver.port=9999 -- \
       flagstat hdfs://<hdfs_master_ip>:8020/mouse_chrM.bam 

Singularity image built on bioconda from BioContainers:

See discussion at bioconda/bioconda-recipes#5144

The bioconda/BioContainers automagic might also make these images available in the Galaxy tool registry. Will look into it.

[fnothaft]

@heuermh can you PR these additions to the docs?

[devin-petersohn]

@heuermh assigning you for now, let me know if you can't make these additions.

[heuermh]

Yep, am working on it