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Installation instructions for Homebrew missing from documentation #1631

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devin-petersohn opened this Issue Jul 25, 2017 · 7 comments

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devin-petersohn commented Jul 25, 2017

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devin-petersohn Jul 25, 2017

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

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devin-petersohn commented Jul 25, 2017

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

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heuermh Jul 25, 2017

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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.

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heuermh commented Jul 25, 2017

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.

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This is for the long docs.

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devin-petersohn commented Jul 25, 2017

This is for the long docs.

@devin-petersohn devin-petersohn added this to the 0.23.0 milestone Jul 25, 2017

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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.

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heuermh commented Jul 25, 2017

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.

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@heuermh can you PR these additions to the docs?

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fnothaft commented Jul 25, 2017

@heuermh can you PR these additions to the docs?

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devin-petersohn Jul 26, 2017

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

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devin-petersohn commented Jul 26, 2017

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

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Yep, am working on it

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heuermh commented Jul 26, 2017

Yep, am working on it

@fnothaft fnothaft closed this in 6573997 Aug 2, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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