Changes between Version 2 and Version 3 of cypress/RunningRWithSingularity

Timestamp:

01/14/26 16:27:24 (5 hours ago)

Author:

Carl Baribault

Comment:

Added section for tidyverse, Seurat

cypress/RunningRWithSingularity

@@ -1 +1 @@
 [[PageOutline]]
 = Running R with Singularity on Cypress =
-The [[https://rocker-project.org/ | Rocker Project]] is a website established to provide docker containers in the form of docker files for the R environment.
+Besides [[https://hub.docker.com | Dockerhub ]], the [[https://rocker-project.org/ | 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 [[wiki:Singularity]].
+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 [[wiki: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.
@@ -62 +62 @@
 https://www.gnu.org/licenses/.
 
-[tulaneID@cypress01-066 rstudio at 15:53:56]$
+[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'''
+
+=== [[https://tidyverse.org/ | 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 ~]$
+}}}
+
+=== [[https://satijalab.org/seurat/ | 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 ~]
+}}}
+