Author: Sergey Lyskov

Application purpose

Provide means to submit Rosetta cluster jobs from Mac/Linux desktop client

Download

To use this application you will need to download latest build for supported platforms could be downloaded from http://graylab.jhu.edu/download/ui/archive/ui/ (ask in #ui RosettaCommons Slack channel for credentials) and unpack archive on your desktop machine.

Setup

When running application for the first time open Preferences menu (command-,) and setup Rosetta Cloud user name and password and preferred PDB viewer. (if you do not have Rosetta Cloud account yet - ask for one #ui RosettaCommons Slack channel )

Overview

Workbench application allow you to submit Task which consist from list of individual Rosetta jobs runs for particular Rosetta version. Each job will be run sequentially from left-most-tab to right-most tab and all previous job guarantee to be finished before next job started.

Rosetta Version

Rosetta version could filed in TaskSubmit dialog could take following values:

Name of the branch, like master. In this case back-end process will use somewhat recent build for this branch (or compile the most recent version for this branch if no previous build is available). Build used will guarantee to be not older then a five-days old.
Name of then branch with colon at the end, like release:. In this case back-end with always use the latest available commit for specified branch.
Git SHA1, like bdd325a0ef3d5d53deef57c12be5ebc859c47304. In this case back-end will try to build specified revision.

Directory Structure of Task during HPC run

When submitted Task started all input files will be places into input/ directory. So for example, if you provided my-pdb.pdb file in you input file set then it could be references in your flag file as input/my-pdb.pdb. Output of previously completed jobs will be placed into <job-name>/ dir. So when you submit multi-stage Task with stages named as 1, 2, 3 you cold access results of previously completed jobs as 1/result-of-job-1-file.extension, 2/result-of-job-2-file.extension, 3/result-of-job-3-file.extension.

Tips

to view PDB file in specified PDB viewer right-click on file then select open from pop-up menu or double click on a file
to open ScoreFile plot for *.score files: right click on file then select open from pop-up menu or double click on a file. In ScoreView you can select which score term to use on X/Y axes, hover over points to view individual scores and double click on point to open particular decoy in your PDB viewer.
to save particular file(s) to disk: select file(s) then right-click on selection and choose save-as
to export all Task files into directory use export all files button on TaskView page
to change run order of Jobs use mouse to click on job-tab and drag it into desired position
current Task queue could be seen at https://ui.graylab.jhu.edu/queue (you will need to use your RosettaCloud login/password to access it)
you can script Task submission/syncing/cancelation though Python by using rosetta_cloud.py script from https://github.com/RosettaCommons/tools.devel/tree/master/rosetta_cloud (see script readme for documentation of how to use it)