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  1. UGENE
  2. UGENE-1779

Cistrome pipeline: RScript validation and installation

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    Details

    • Sprint:
      DEV-2013/08/15, DEV-2013/08/22, DEV-2013/12/05
    • Affect Type:
      Userdefined

      Description

      Some tools of the Cistrome pipeline use Rscript and Bioconductor libraries.
      Currently, the requirements are the following:
      • "R" software environment must be installed
      • "R" must be added to the PATH environment variable
      • Additional "Bioconductor" packages must be installed using the "installRpackages.R" script from the Cistrome Configuration Package. (Note that the script was not modified, so there is no need to re-launch it, if the packages had already been installed on the system).

      There must be a simpler way to setup R and it libraries in UGENE.
      Add additional complex validation which does the following:
      1. Checks if RScript is installed and can be run
      1*. If it is not installed show a window with a relevant message and a link to R installation page.
      2. Check if all libraries of installRpackages.R are installed
      2*. If any of them are not installed shows the installation window which requires to enter admin password (to run sudo). Also is shows message that packages will be installed with sudo. After that it installs the packages
      3. If all validations above are successful shows 'no errors' validation status

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            Assignee:
            atiunov Aleksey Tiunov [X] (Inactive)
            Reporter:
            vaskin Yura Vaskin
            Watchers:
            1 Start watching this issue

              Dates

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              Updated:
              Resolved:

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                Estimated:
                Original Estimate - 6 hours
                6h
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                Remaining Estimate - 6 hours
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