iPlant – Advanced workshop

“API for scalable science” – Matt Vaughn, John Fonner





Install Docker (I’m running OSX. See other instructions for Linux and Windows, although there were challenges with Windows users in the workshop). Docker is solution to binaries and configurations, etc. specific to hardware. Cool because hardware goes out of date, need to move software to keep working. VM – one way to backup and move software and storage – are snapshot of entire operating system, big and heavy. Literally booting a computer. With docker containers, all containers share kernel. Disk images layered. (Provisionally based on Linux.) Coupled with services that allow publishing images in layers. If wanting to automate server production, can have orchestrated by Docker. Pull down base image, apache installation. Platform as service, versionable. Integration between hub and github and other public source control services. It is the recipe for building a web server. Useful for sharing code and workflows between people with different versions of software. Want Docker to follow recipe so software worries can be solved behind the scenes, allowing people to focus on using the software.


iPlant with Agave platform, moving to Docker. (Can only be done on system you own. So, iPlant sysadmin will run this from backend, but not users.) Integrates storage and computing into unified environment and access all same way on web server available to public.

Idea is that “Scientists, with a  few exceptions, are not trained programmers.” “Science is no longer done in a sandbox.” Meaning that large interdisciplinary research needed to answer one question. Data not all living in one place. Docker allows for programability. Security issues, Docker will need to run user namespace  to allow users to run custom Docker images.

Interactive Tour

Launch Agave CLI container:

Screen Shot 2015-09-22 at 4.47.47 PM

Get authorization tokens with iPlant login account.

Storage systems avail, including ncbi – can edit to point to specific directory location:

Screen Shot 2015-09-23 at 11.44.04 AM

Look through api tools, e.g. files-list

Screen Shot 2015-09-23 at 11.59.57 AM

did not work for ncbi:

Screen Shot 2015-09-23 at 11.57.41 AM

Use this for advanced system management:


Screen Shot 2015-09-23 at 11.59.57 AM

and list all iplant training files:

Screen Shot 2015-09-23 at 12.01.29 PM

Make file and upload:

Screen Shot 2015-09-23 at 12.02.47 PM

Permission bug with files creation and getting:

Screen Shot 2015-09-23 at 12.08.55 PM

Apps, here are some: account-toolname-system-version-versionnum

Screen Shot 2015-09-23 at 12.12.23 PM

Can do jobs template (see tutorial under ‘Jobs’).

Can search for name and get list of results:

Screen Shot 2015-09-23 at 12.16.56 PM

About Lisa Johnson

PhD candidate at UC Davis in Molecular, Cellular, and Integrative Physiology
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