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Scripts and JSON definitions for deploying iReceptorPlus systems and apps in Tapis.

Tapis (formerly called Agave) is an open source, science-as-a-service API platform.

• systems: JSON definitions for execution/storage systems.

• apps: JSON definitions and application wrapper for tools.

This repository has a corresponding docker image which can be used to access Tapis. Theimage contains the Tapis command-line interface (CLI),agavepy python library, and otheruseful tools. Immune repertoire analysis tools do not reside within this image, as theywill be provided in separate images that can be run on HPC.

To use the docker image, you need these requirements:

• Docker Desktop installed on your computer.

• VDJServer user account.

Pull down the latest image from docker hub.

docker pull ireceptorplus/tapis

When you initialize Tapis and login with your VDJServer user account, Tapis returns anauthentication token for all subsequence requests. This token is managed for you and issaved to disk. However, by default, files created in the docker container are deleted whenexiting the container. To avoid having to initialize Tapis every time you use the docker image,we mount a local directory into the docker container where the files are saved.

# Create a local directory to hold Tapis initialization and token datamkdir tapis-token

Run a bash shell and initialize Tapis. The initialization will ask a few questions.When it asks for the tenant name, pickvdjserver.org. It will then ask for your VDJServerusername and password for login.The prompts for container registry access and git server access can be left blank orleft as the provided defaults.

docker run -v $PWD/tapis-token:/root/.agave -it ireceptorplus/tapis bashtapis auth init

With Tapis initialized, you can now try some commands:

# help for the Tapis CLItapis --help# show your authentication tokentapis auth show# refresh your authentication token when it expirestapis auth tokens refresh# create a new authentication token (requires password)tapis auth tokens create# list of systems availabletapis systems list# list of apps availabletapis apps list# list files in the irplus directory (you need permission to view)tapis files list agave://data.vdjserver.org/irplus

While the docker image provides a copy of this repository, any changes you make to files within the imagemight be lost, so clone this repository to your local system and mount it in the dockercontainer for doing development. You will generally want to perform git commands and usean editor outside of docker.

# clone the repositorygit clone https://github.com/ireceptor-plus/tapis.gitcd tapisgit submodule update --init --recursive# run docker with both your tapis token and source directories mounteddocker run -v $PWD/tapis-token:/root/.agave -v $PWD/tapis:/work -it ireceptorplus/tapis bash# access local app developmentcd /work

The hackathon of Sep 2-4 provided a tutorial presentation and hands-on session for appdevelopment. Here are somenotes and aJupyter notebook put together by Marco Amaro Oliveira.