HPC Functionality

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Bioclipse Project
Wiki page last updated:2011-10-17
Repo URL:https://github.com/bioclipse/bioclipse.hpc
Idea is to extend Bioclipse with functionality to connect to Uppmax/Uppnex resources via SSH.

Remote System Explorer


Execute commands remotely

Source code

Misc stuff

SWT/JFace reading

Progress log

  • Samuell 11:24, 10 June 2011 (UTC): Realized I have to read up more on the extensions points (also the RSE eclipse plat form ones)
  • Samuell 12:33, 10 June 2011 (UTC): Ah, found an open source extension to RSE, which might provide good example code: http://jaxenter.com/tool-for-extending-eclipse-rse-10278.html
  • Samuell 13:09, 10 June 2011 (UTC): Realized I should study the Widgets API for how to code file selection dialog.
  • Samuell 14:24, 13 June 2011 (UTC): Finally found that they mention in the FAQ where to find the material to get started - in the EclipseCon 2008 example material. Some links are broken though, but some of the 2008-links on this page works.
  • Samuell 18:15, 14 June 2011 (UTC): Someone else trying to get up a remote file dialog in RSE, at this forum thread.
  • Samuell 13:42, 29 July 2011 (UTC): Renamed extension net.bioclipse.uppmax -> net.bioclipse.hpc. Otherwise status is: Having got remote file selection dialog to work earlier. Big code cleaning session today. Working on wizard page for SBATCH config.
  • Samuell 10:36, 2 August 2011 (UTC): Updated the RSE bug that gives "pipe closed" if I do too fast consecutive readLine() calls on the result from executed remote commands: http://tinyurl.com/rse-readline-bug
  • Samuell 14:15, 3 August 2011 (UTC): The job config wizard now produces an SBATCH file. There's still work to be done on validating the different SBATCH options, and probably add a nicer widget for specifying job time.
  • Samuell 14:17, 3 August 2011 (UTC): I realized now how to handle the UPPMAX module system ... Galaxy ToolConfigs should be stored together with the module system, and the first thing to do in the wizard, is to choose module (info about module to be provided by the fimsproxy script), and when module has been chosen, the wizard will show which tools for which there is toolconfig files available ... and after a tool is chosen, the toolconfig file is read and parsed. Yep, think that's how to do it ...
  • Samuell 17:38, 5 August 2011 (UTC): Got the preference page working + a dialog showing on startup, to set the same properties (wich checkbox to choose whether to show it on startup).
  • Samuell 11:27, 12 August 2011 (UTC): Posted question on StackOverflow: "How to programmatically refresh an Eclipse view, or RSE file subsystem?"