2.0 Build 5

  • This version fixes a problem that prevented the workbench to start on Mac (introduced with Build 3). The linux build was unaffected.
  • Since build 5, we are starting to distribute languages for the workbench as MPS plugins. This makes it possible to use NYoSh workbench languages in the Jetbrains MPS distribution. The plugins are smaller than the complete standalone distribution and can be obtained from the MPS plugin repository. Users are notified of updates to the plugins. You can obtain plugins from http://campagnelab.org/software/mps-plugins/, or from the Jetbrains MPS plugin repository when they have cleared moderation.
  • We have added several languages to help register filesets: organism and platforms attributes in fileset registration now offer auto-completion. This is done with language composition and can be turned on/off by importing these languages or not.
  • Build 5 includes support for multiple users in the fileset library and provides a language to refer to users. This was needed to create pre-defined users that will be used during the NYoSh workshop.

This build includes the following detailed change items:

  • Autocompletion for organism names. (DONE)
  • Autocompletion for platform names + paired directions (DONE).
  • Fastq files must  be gzipped in test-data (DONE)
  • Return an error when the registration of fileset fails (feedback) (DONE)
  • SharingTool has to import related instances if the instance to share is of type JOB_METADATA (same behavior as the ImportTool) DONE
  • Prepare 2 FASTQ files as data archive (Pickrell) DONE
  • Fix issue with fileset manager client name. hostname+solution name+model. Done
  • Test that Reads > Alignment > Analysis works. Done.
  • Test Multi-tool for alignments. Done.
  • Submit multiple alignments or Diff Exp. (Done)
  • Fetch plugins from a location different than the submission machine. Add two optional parameters to job that locate the plugin repo location. Possible implementation: Derive a sub-concept of plugin repository that provides a hostname and remote path on the host. Add PluginRepo methods to retrieve these values in the same way from the current PluginRepo or sub-concept (let’s call it DualPluginRepo). Auto-completion will provide the mechanism to switch from one to the other. It is a cleaner design than adding optional fields on the current plugin repo because it removes conditional code on clients (e.g., no need for ifs when using the repo, always get the host and remote path attribute). [Done.]
  • Implement Sharing tool. Done.