lipcomputing/ipyrad repository overview

⁠Docker: ipyrad

Docker to run ipyrad

Installation and user manual is found here:

• http://ipyrad.readthedocs.io/index.html⁠

Tags correspond to the version of ipyrad, currently:

• latest: ipyrad 0.7.30

⁠Usage udocker

udocker is a user client tool to run docker containers without docker. It's aimed at running applications in user space without root or admin previledges.

udocker resources can be found in:

• Repository: https://github.com/indigo-dc/udocker⁠
• Installation manual: https://github.com/indigo-dc/udocker/blob/master/doc/installation_manual.md⁠
• User manual: https://github.com/indigo-dc/udocker/blob/master/doc/user_manual.md⁠
• Paper open access: https://doi.org/10.1016/j.cpc.2018.05.021⁠

A summary of using udocker to run ipyrad follows:

mkdir -p ~/bin
curl https://raw.githubusercontent.com/indigo-dc/udocker/master/udocker.py > bin/udocker
chmod u+rx bin/udocker
udocker install
udocker pull lipcomputing/ipyrad:0.7.30
udocker create --name=ipyrad lipcomputing/ipyrad:0.7.30

If you are running with multiple threads or processes, OpenMP or OpenMPI, better performace is acheived with udocker F mode:

udocker setup --execmode=F1 ipyrad

If you have input files to pass to the container to run the application, for example in ~/input, you can run:

udocker run -v  $PWD/input:/home ipyrad ipyrad -n iptest

⁠Usage Docker

Pull the docker image

docker pull lipcomputing/ipyrad

Run ipyrad: get the help usage

docker run lipcomputing/ipyrad ipyrad -h

Or you can run the container in interactive mode:

docker run -it lipcomputing/ipyrad /bin/bash

# ipyrad -h

Other examples in: http://ipyrad.readthedocs.io/outline.html⁠

You can map a directory into the docker container for input and output

If you local dir is pwd, you can run:

PWD=`pwd`
docker run -it -v ${PWD}:/home/test lipcomputing/ipyrad /bin/bash
# cd /home/test

Such that if you have you input files in your host machine, they will be available in the directory /home/test inside the container, as well as output files produced in that dir by running the application inside the container they will be available when you exit, in that directory pwd.

⁠License

GNU GPL v3

⁠Author Information

Mario David: [email protected]⁠

LIP Lisbon: http://www.lip.pt⁠

Indigo DataCloud: https://www.indigo-datacloud.eu/⁠