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Installer for SCR workers

Installer for SCR workers

Apr 05, 2012
  • Latest version of R
  • rSCR package and its dependencies
    • First make sure bioconductor is installed.  To install the core bioconductor packages do the following
      • source("http://bioconductor.org/biocLite.R")
      • biocLite()
      • biocLite(c("affy","digest"))
    • Then install the non-BioC libraries we need
      • install.packages(c("RCurl","RJSONIO"))
      • note you'll be prompted to select a repository.  Just select the one closest to you.  You're not transferring much over the wire so don't be too picky.

    • Next we need to install the Synapse Client and rSCR packages.  Install the ones below:

      • SynapseClient
      • rSCR
  • JAVA .jar file
    • simply provide a public link that people can download
  • Properties file
    • All paths are relative.
    • Need to get people set up with user accounts and encrypted passwords.  Simply link to instructions to do this.
  • activity.sh
    • need to set paths for 

      • -Dorg.sagebionetworks.stack.configuration.url=file:///Users/brig.mecham/Documents/workspace/swf/prodLive-sageCommonsWorkflow.properties \

        -javaagent:/Users/brig.mecham/Documents/workspace/swf/aspectjweaver-1.6.10.jar \

        -cp /Users/brig.mecham/Documents/workspace/swf/sageCommonsWorkflow-0.12-SNAPSHOT.jar \

  • initiator.sh
    • don't think we need this installed remotely
  • decider.sh
    • ditto