Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Installation instructions for Homebrew missing from documentation #1631

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

Installation instructions for Homebrew missing from documentation #1631

devin-petersohn opened this issue Jul 25, 2017 · 7 comments
Assignees
Labels
Milestone

Comments

@devin-petersohn
Copy link
Member

@devin-petersohn devin-petersohn commented Jul 25, 2017

No description provided.

@devin-petersohn
Copy link
Member Author

@devin-petersohn devin-petersohn commented Jul 25, 2017

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

@heuermh
Copy link
Member

@heuermh 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.

@devin-petersohn
Copy link
Member Author

@devin-petersohn 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
@heuermh
Copy link
Member

@heuermh 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.

@fnothaft
Copy link
Member

@fnothaft fnothaft commented Jul 25, 2017

@heuermh can you PR these additions to the docs?

@devin-petersohn
Copy link
Member Author

@devin-petersohn devin-petersohn commented Jul 26, 2017

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

@heuermh
Copy link
Member

@heuermh 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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
Linked pull requests

Successfully merging a pull request may close this issue.

None yet
3 participants
You can’t perform that action at this time.