Install R and Python packages from the local Sandbox repository

Many commonly used R and Python packages are pre-installed in the Sandbox IVM. Users can install additional R and Python packages from the local Sandbox repository. It contains less frequently used packages and packages that may conflict with others.

Users can request new packages to be pre-installed in the Sandbox IVM or added to the local Sandbox repository (please see policy).

R packages

List R packages available in the local Sandbox CRAN repository using R

The Sandbox IVM has been pre-configured to use the local Sandbox CRAN repository. The available.packages() R command can be used to list the available packages in the local Sandbox CRAN repository.

Use the following command to list all available packages and their versions:

available.packages()[,c("Package","Version")]

You can search available packages by name. For example, use the following command to list all packages that start with 'Bi':

p <- available.packages()[,c("Package", "Version")] 
c <- grepl("^Bi", p[,c("Package")], ignore.case=TRUE) 
p[c,]

The available.packages()command returns other columns as well. You can list them all using the colnames command:

colnames(available.packages())

List R packages available in the local Sandbox CRAN repository using the terminal

You can list packages using the R command line program with the -e option following other instructions in the previous section.

List all packages:

R -e 'available.packages()[,c("Package","Version")]'

Search packages by name:

R -e 'p <- available.packages()[,c("Package", "Version")];c <- grepl("^Bi", p[,c("Package")], ignore.case=TRUE);p[c,]'

You can also directly list the packages in the local Sandbox CRAN repository:

ls /usr/finngen-repos/cran/source/src/contrib

Install R packages from the local Sandbox CRAN repository

The Sandbox IVM has been pre-configured to use the local Sandbox CRAN repository. Use the install.packages("package name") R command to install packages from the local Sandbox CRAN repository.

For example, the following command installs the Biobase package:

install.packages("Biobase")

Packages are installed in your Sandbox IVM persistent disk. The exact location depends on the R version, for example, /home/ivm/Rx86_64-pc-linux-gnu-library/4.3. Installed packages are automatically detected by R only from this location. When using a different version of R, you may need to use the .libPaths() variable to define the location of the package (more information is available here). You can also install the same package for different R versions.

List available R packages in the local Sandbox CRAN repository outside the Sandbox

It is possible to list the available R packages outside Sandbox by using buckets.

R packages are available in the following bucket:

gs://fg-production-master_cran/source/src/contrib

You can see the contents of the bucket using the cloud console:

https://console.cloud.google.com/storage/browser/fg-production-master_cran/source/src/contrib;tab=objects?project=fg-production-master

or the gsutil command line program:

gsutil ls gs://fg-production-master_cran/source/src/contrib

Python packages

List Python packages available in the local Sandbox PyPI repository using the terminal

The Sandbox IVM has been pre-configured to use the local Sandbox PyPI repository: https://pypiserver.app.finngen.fi/. It contains packages for both Python 2 and Python 3. FinnGen uses the pip program to install Python packages in the Sandbox.

Use the following command to list available Python 2 packages:

python -m pip list

Use the following command to list available Python 3 packages:

python3 -m pip list

Install Python packages from the local Sandbox PyPI repository using the terminal

Use the following command to install a Python 2 package:

python -m pip install <packagename>

Use the following command to install a Python 3 package:

python3 -m pip install <packagename>

You can also install Python packages in virtual environments. Instructions on how to create a virtual environment are available here.

List available Python packages in the local Sandbox PyPI repository outside the Sandbox

It is possible to list the available Python packages outside Sandbox by using buckets.

Python 2 packages are available in the following bucket:

gs://fg-production-master_pypi/python2

Python 3 packages are available in the following bucket:

gs://fg-production-master_pypi/python3

You can see the contents of the buckets using the cloud console:

https://console.cloud.google.com/storage/browser/fg-production-master_pypi/python2?project=fg-production-master

https://console.cloud.google.com/storage/browser/fg-production-master_pypi/python3?project=fg-production-master

or the gsutil command line program:

gsutil ls gs://fg-production-master_pypi/python2
gsutil ls gs://fg-production-master_pypi/python3