lightweight hpc client based on galaxy tool configs - my lightning talk at gcc2013
DESCRIPTION
A lightweight HPC client, that is not based upon the full Galaxy stack but mainly the Tool config files, and that might be a complementary solution to centers who are providing both Galaxy and shell-based access to their cluster. Instead of running a web server, it runs locally on the users machine (as a java-application) and in the background accesses the cluster via SSH, in the same way as you would have done with the terminal. Using the tool configs, a wizard is presented to the user for configuring SLURM sbatch files. After a job is submitted, jobs can be viewed in a separate view, and the user can also manage files on the cluster via the in-built file-browser, genome-viewer etc, without the full Galaxy stack. But, if the user wants to run an own Galaxy instance on the cluster, the client can also do the tricky SSH tunneling magic for the user, and present the galaxy web user interface in a built-in browser.TRANSCRIPT
“Lightweight” HPC Client Leveraging Galaxy Tool configs
Samuel Lampa, UPPMAX, Uppsala [email protected]
twitter.com/smllmp
Background
● Want to re-use tool wrapping work already done in Galaxy
● Sysadmins with … strict … policies● Only accepted authentication: SSH● :/
Solution
● Use SSH!● Use (Galaxy) Toolconfigs!● :)
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Take home messages / questions
● “light-weight” helper tool, using normal HPC
● Teaches (normal) HPC usage
● Ways to make tool configs more declarative?
● We will (try to) use Galaxy in the normal way too!
Youtube Demo:tinyurl.com/hpcclient
Samuel Lampa, UPPMAX, Uppsala [email protected]
twitter.com/smllmp
Status:Proof of concept