Page Comparison

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• JupyterHub Server
  
  • Clicking "Logout" in JupyterHub server does not work – it displays a "404 page not found" error.
• Command-line programs
  
  • The following programs may not be working currently, but we are working to correct them asap.
    • bcl2fastq
    • gossamer
    • glimmer2
  • On the EDU pod, the 3rd party programs used by Josh Beckham's FRI stream (e.g. Gold) are not yet working.
  • A few R packages may not be working correctly on some upgraded machines.   These may include:
    • Seurat
    • Signac
    • ChIPseeker
• Storage server access
  • The rssh program that allows direct access to the shared storage server via SSH (e.g. scp, rsync, sftp) is not available in Ubuntu 20.04. We are actively working to implement a suitable replacement. Meanwhile, files can be transferred to/from the storage server through any of a POD's compute server via scp, rsync, sftp.

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All compute servers have both web-based R Studio Server and JupyterHub Server installed. A menu allowing you to select from the installed web-based applications is available by specifying any POD compute server name in a web browser; for example: https://gsafcomp01.ccbb.utexas.edu/

Also see below for changes to command-line versions of R and Python.

RStudio differences

The version of R in RStudio under Ubuntu 18.04 was either R 3.6.1 or R 4.0.3, as documented at Web-based RStudio and JupyterHub software. Servers with RStudio using R 4.0.3 will still use that version, although we plan to upgrade the R version to R 4.2 going forward. However the servers using R 3.6.1 will now run R 3.6.3. We do not anticipate that this will affect user-installed packages, but if you run into issues, move your ~/R directory out of the way as described at Global package installation conflicts, then re-install your package(s). If the problem persists please Contact Us.

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• For programs downloaded as pre-built prebuilt binaries, check the maintainer's website for a version compatible with Ubuntu 20.04.
• For programs downloaded as source and built by you, move the previous binaries (often in ~/bin or ~/.local/bin), then perform a clean build from existing (or updated) source code.

R and Python versions

After the upgrade, R and Python versions will be as follows:

• Python
  • Default comand-line python still 2.7
  • Default python3 3.8.10, as is the Python in JupyterHub Server
  • Python 3.6 no longer available ?
• R
  • Default command-line R will be 4.0.1 (it is currently 3.6.1)
    • also available explicitly as R-4.0.3
  • R 3.6.3 will be accessible from the command line as R-3.6.3
  • RStudio Server R will be either 3.6.3 (if 3.6.1 previously) or still 4.0.1
  • R 3.4 and 3.6.1 no longer available

If you run into problems running Python or R programs that used to work before:

• For R packages, your local installations are in your ~/R directory. Rename that directory (e.g. to ~/R.bak) so you can refer to it to see which packages you installed. You may then need to re-install any packages you need that are not already installed globally (you can check this by doing library(<module_name>) in R).
  • See above for the different R versions available in RStudio Server.
• For Python packages, your local installations are in your ~/.local/lib/python2.7 or ~/.local/lib/python3 directories. Rename those directories (e.g. to ~/.local/lib/python2.7.previous) so you can refer to it to see which packages you installed, then re-install those packages.

Also see How RStudio Server and JupyterHub Server changes may affect you.