diff --git a/docs/09_reproducibility_IV.md b/docs/09_reproducibility_IV.md index 74a7067e0..f935e402c 100644 --- a/docs/09_reproducibility_IV.md +++ b/docs/09_reproducibility_IV.md @@ -1,4 +1,4 @@ -# Singularity +# Containers and the HPC ``` Material is coming! @@ -19,4 +19,46 @@ Material is coming! : .-. : : .-. : '........' (_________): .-. :`-' : '-' : : '-' : : '-' : '._ _.' '._ _.' '._ _.' -``` \ No newline at end of file +``` + +!!! Success "Expected Outcomes" + - Being able to log onto the HPC and start an interactive node + - Know basic HPC related commands + - Execute containerized code through Singularity/Apptainer + - Being able to search and load specific software + - Execute NextFlow scripts on the HPC + + +## HPC: The Basics + +Resources: + - https://uarizona.atlassian.net/wiki/spaces/UAHPC/pages/75990696/User+Guide + - https://uarizona.atlassian.net/wiki/spaces/UAHPC/pages/75990091/HPC+High+Performance+Storage +### Logging onto the HPC +### Choosing the System +### Checking Available Resources +## Launching an Interactive Node + +Resources: + - https://uarizona.atlassian.net/wiki/spaces/UAHPC/pages/75989825/Interactive+Jobs + +### SLURM and Commands + +Resouces: + - https://uarizona.atlassian.net/wiki/spaces/UAHPC/pages/75989875/Running+Jobs+with+Slurm + - https://uarizona.atlassian.net/wiki/spaces/UAHPC/pages/75989486/Cheat+Sheet + +## Singularity/Apptainer +### Executable Commands + +Resources: + - https://cc.cyverse.org/singularity/intro/ + - https://cc.cyverse.org/singularity/hpc/ + - https://cc.cyverse.org/singularity/advanced/ + +## NextFlow on the HPC + +Resources: +- https://training.nextflow.io/basic_training/executors/ +- https://lescailab.unipv.it/guides/eos_guide/use_nextflow.html +- Example: https://nf-co.re/smartseq2/dev/docs/usage \ No newline at end of file