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Install packages in CERNBox

LCG releases on CVMFS incorporate new packages quite frequently, so if you think there is a missing package that can be potentially useful for a significant number of users, please let the SWAN team know and contact the librarians directly.

On the other hand, you can install packages on your CERNBox and, if necessary, configure your environment to pick them up in SWAN.

Python

A typical case is the installation of Python packages, which requires to run pip from a SWAN terminal:

pip install --user package_name

If this fails because you are trying to install an updated version of a package that already exists in CVMFS, you will need to add the --upgrade flag.

Then, it would be necessary to add the local installation path to PYTHONPATH, by creating a bash startup script that configures that variable (don't forget to call this startup script in the session configuration menu):

export PYTHONPATH=$CERNBOX_HOME/.local/lib/python3.5/site-packages:$PYTHONPATH

As a result of performing the aforementioned steps, the package will be installed on your CERNBox and it will be picked by any notebook you open after that. Since the package is on your CERNBox, it will be also available in any new session you start in SWAN.

R

You can also install R packages on your CERNBox. For that, from a SWAN terminal, create a subdirectory on your CERNBox home directory using the next command: mkdir -p ~/Rpackages

Next, still from the SWAN terminal, open the R interpreter and run the next command to install your package (replace "package_here" by the name of your package): install.packages('package_here', repos='http://cran.rstudio.com/',lib = '~/Rpackages')

Finally, from your R notebook, you will be able to use your package after running the following two commands in a cell: .libPaths(c(.libPaths(), "~/Rpackages")) require(installed_pkg,lib='~/Rpackages',character.only = TRUE)