Running R with Singularity on Cypress

Besides ​ Dockerhub , the ​ Rocker Project is a website established to provide docker containers in the form of docker files specifically for the R environment.

In order to use any of those docker files on Cypress, we'll need to construct a container file - usually with .sif file extension - suitable for use with Singularity on Cypress. For reference in the following, see Singularity.

Here's the sequence of commands to create and simply test a container file for the latest available R version - as provided the above website.

Start the interactive session

First, start an interactive session.

For Workshop : If your account is in the group workshop, please use the following.

[tulaneID@cypress1 ~]$idev --partition=workshop7 -c 2 # request 2 cores in the partition workshop7
Requesting 1 node(s)  task(s) to normal queue of workshop7 partition
1 task(s)/node, 2 cpu(s)/task, 0 MIC device(s)/node
Time: 0 (hr) 60 (min).
0d 0h 60m
Submitted batch job 3287405
JOBID=3287405 begin on cypress01-060
--> Creating interactive terminal session (login) on node cypress01-060.
--> You have 0 (hr) 60 (min).
--> Assigned Host List : /tmp/idev_nodes_file_tulaneID
Last login: Tue Jan 13 11:58:39 2026 from cypress1.cm.cluster
[tulaneID@cypress01-060 ~]$

Non-workshop

[tulaneID@cypress1 ~]idev --partition=centos7 # start an interactive session in the partition centos7
Requesting 1 node(s)  task(s) to normal queue of centos7 partition
1 task(s)/node, 20 cpu(s)/task, 0 MIC device(s)/node
Time: 0 (hr) 60 (min).
0d 0h 60m
Submitted batch job 3288388
JOBID=3288388 begin on cypress01-066
--> Creating interactive terminal session (login) on node cypress01-066.
--> You have 0 (hr) 60 (min).
--> Assigned Host List : /tmp/idev_nodes_file_tulaneID
Last login: Tue Jan 13 14:09:07 2026 from cypress2.cm.cluster
[tulaneID@cypress01-066 ~]$

Construct and check the container image file

Then proceed as follows to construct the .sif container image file and check the R version.

[tulaneID@cypress01-060 ~]$module load singularity/3.9.0 # load the singularity module
[tulaneID@cypress01-060 ~]$singularity pull docker://rocker/r-base:latest # takes a few minutes to construct file r-base_latest.sif
...
[tulaneID@cypress01-060 ~]$singularity exec r-base_latest.sif R --version # check the version of R
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.

[tulaneID@cypress01-066 ~]$

Other R container images available via the Rocker Project and Dockerhub

Keep in mind that the following examples assume that you've already entered an interactive session using idev —partition=centos7.

For Workshop: Use idev —partition=workshop7 -c 2

​ tidyverse

[tulaneID@cypress01-057 ~]$singularity pull docker://rocker/tidyverse:latest
...
[tulaneID@cypress01-057 ~]$singularity exec tidyverse_latest.sif Rscript -e 'packageVersion("tidyverse")'
[1] '2.0.0'
[tulaneID@cypress01-057 ~]$

​ Seurat

[tulaneID@cypress01-057 ~]$singularity pull docker://satijalab/seurat:latest
...
[tulaneID@cypress01-057 ~]$singularity exec seurat_latest.sif Rscript -e 'packageVersion("Seurat")'
[1] '4.3.0'
[tulaneID@cypress01-057 ~]