diff --git a/script_singularity b/script_singularity new file mode 100644 index 0000000..84ecad9 --- /dev/null +++ b/script_singularity @@ -0,0 +1,22 @@ +STEPS FOR RUNNING MIRAI ON A REMOTE HPC WITHIN A SINGULARITY CONTAINER + +Transfer .tar file to remote HPC directory +$ rsync -avPz oncoserve_mirai_0.3.1.tar foo@host: PATH_T0_DIR + +Activate Singularity module on HPC: +$ module load gcc/8.3.0 +$ module load singularity/3.6.4 + +Covert .tar file to singularity image (writeable sandbox format used here) +Within the oncoserve_mirai_0.3.1.tar file directory: +$ singularity build --disable-cache --sandbox oncoserve_mirai_0.3.1.simg docker-archive://oncoserve_mirai_0.3.1.tar +"--disable-cache" option only necessary if encountering disk space limitation for cache or unable to change cache directory: + +RUNNING SINGULARITY SHELL WITH SANDBOX IMAGE IN PLACE: + +$ singularity shell --bind PATH_TO_DATA_DIR:/data oncoserve_mirai_0.3.1.simg /bin/zsh +this takes you into the singularity shell + +: +Singularity> cd /root/OncoNet/ +Singularity> pip install -r requirements.txt