Astrocyte Container Images

A skeleton repo acting as a host registry for various images used in Astrocyte.

R

The R images that are used by Astrocyte CLI and Astrocyte to build and run the R Shiny of the Vizapp.

These images were built based on the Centos7 and the official release of different R versions. The default CRAN were set to https://cloud.r-project.org and https://cran.rstudio.com through Rprofile.site. R packages 'BiocManager', 'shiny', 'shinyFiles', and 'devtools' were installed by default as well. The users could customize the location of their libraries by modifying the environment variable R_LIBS. The UT Southwestern proxy settings are included as bellow. To run the containers outside the UTSW network, the environment variables need to be changed.

http_proxy=http://proxy.swmed.edu:3128/ 
https_proxy=http://proxy.swmed.edu:3128/ 
no_proxy="*.swmed.edu,*.swmed.org,*.utsouthwestern.edu,localhost,127.0.0.1/8"

The Astrocyte workflow developers are suggested to use these containers to develop and test there R shiny vizapps. These containers are available through the the R/x.x.x-img modules on BioHPC as well.

Singularity

The inside container of Singularity. It was built with the --without-suid option to disable the user namespaces. See here and here for more details.

Nextflow

The container of nextflow.