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Overview
Before summer of 2019, BRCF POD compute and storage servers were running Ubuntu Linux version 14.04 LTS (Long Term Support), which was released in 2014 with 5 years of support/updates. As of April 2019, updates for Ubuntu 14.04 were frozen and no longer available in the standard repositories. As a result, all BRCF POD servers need to be migrated to a newer Ubuntu LTS release. We selected Ubuntu 18.04 LTS, as it will be supported until April 2023.
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- July 24 - Chen/Wallingford and Iyer/Kim PODs
- July 31 - Dickinson/Cambronne, Ochman, Wilke and EDU PODs
- Aug 7 - Georgiou/WCAAR, GSAF, Lambowitz/CCBB and Marcotte PODs
How the compute server O/S upgrade may affect you
There are two categories of programs installed on compute servers:
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These can be binaries built from source, or in the case of Python/Pyton3 and R/R Studio server, add-on packages.
Missing globally-installed programs
Compute servers under the previous Ubuntu 14.04 release included a layer of bioinformatics software called BioLinux 7. That layer is not available for Ubuntu 18.04. We have attempted to globally install the most important BioLinux 7 tools under Ubuntu 18.04; however some may be missing.
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We are working to update our POD Software Information to reflect globally-installed software available under Ubuntu 18.04, but it currently reflects only the 14.04 environment.
Incompatible user-installed programs
Programs you installed under Ubuntu 14.04 may no longer work.
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- For programs downloaded as pre-built binaries, check the maintainer's website for a version compatible with Ubuntu 18.04.
- 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.
- For R packages, your local installations are in your ~/R directory. Rename that directory (e.g. to ~/R.previous) so you can refer to it to see which packages you installed, then re-install those packages.
- 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.
Notes on R Studio Server and JupyterHub Server
In our new Ubuntu 18.04 environment, all compute servers have both web-based R Studio Server and JupyterHub Server installed.
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