# SAIGE in a singularity container @UPPMAX https://saigegit.github.io/SAIGE-doc/docs/Installation_docker.html ## Installation - pulling the container ```bash= # ssh to Rackham ssh user_id@rackham.uppmax.uu.se # Pelle # ssh user_id@pelle.uppmax.uu.se # Disable apptainer cache export APPTAINER_DISABLE_CACHE=true # navigate to a folder in your project cd /proj/... # Pull the container apptainer pull docker://wzhou88/saige:1.5.0 ``` ## Running the tool ### Running interactively ```bash= #Enter the container apptainer shell /full_path_to/saige_1.5.0.sif # navigate to your data folder and run as in the documentation step1_fitNULLGLMM.R --help ``` > Note: while in the container, the current shell has only the tools available in the container i.e. many common tools and editors are not available. ### Running non-interactively ```bash= # Navigate to your data folder apptainer exec /full_path_to/saige_1.5.0.sif step1_fitNULLGLMM.R --help ``` > Effectively, each command needs to be preceeded by `apptainer exec /full_path_to/saige_1.5.0.sif` which means to run the rest in the specified container. ## Contacts: - [Pavlin Mitev](https://katalog.uu.se/profile/?id=N3-1425) - [UPPMAX](https://www.uu.se/en/centre/uppmax) - [AE@UPPMAX - related documentation](/8sqXISVRRquPDSw9o1DizQ) ###### tags: `UPPMAX`, `SAIGE`, `RT317852`