diff --git a/docs/execution.md b/docs/execution.md new file mode 100644 index 0000000..d742058 --- /dev/null +++ b/docs/execution.md @@ -0,0 +1,111 @@ +**weave** is capable of automatically distributing its pipeline jobs across a slurm cluster. The context for it's initial execution can be varied as well. + +The context is also centrally related to the configuration and setup of a particular cluster. Right now weave is configured to work with NIH clusters **skyline**, **biowulf**, and **bigsky**. + + +Typical contexts of execution include: + +# srun (real time execution) (non-interactive) + +The **weave** pipeline can be triggered from a head node in a non-interactive fashion: + +## Bigsky/Skyline + +!!! Note + Dependency files for skyline and bigsky differ + Bigsky: `/gs1/RTS/OpenOmics/bin/dependencies.sh` + Skyline: `/data/openomics/bin/dependencies.sh` + +```bash +source ${dependencies} +srun --export=ALL "weave run [keyword args] ${run_id}" +``` + +!!! Note + srun (by default)[https://slurm.schedmd.com/srun.html#OPT_export] exports all environmental variables from the executing environment and `--export=ALL` can be left off + +## Biowulf + +```bash +srun --export=ALL "module load snakemake singularity; weave run [keyword args] ${run_id}" +``` + +# srun (real time execution) (interactive) + +## Bigsky/Skyline + +!!! Note + Dependency files for skyline and bigsky differ + Bigsky: `/gs1/RTS/OpenOmics/bin/dependencies.sh` + Skyline: `/data/openomics/bin/dependencies.sh` + +```bash +> # +srun --pty bash +> # +source ${dependencies} +weave run [keyword args] ${run_id} +``` + +## Biowulf + +```bash +> # +sinteractive +> # +module purge +module load snakemake singularity +weave run [keyword args] ${run_id} +``` + +Biowulf uses environmental modules to control software. After executing the above you should see a message similar to: + +> [+] Loading snakemake 7.XX.X on cnXXXX
+> [+] Loading singularity 4.X.X on cnXXXX
+ +# sbatch (later time execution) + +## Bigsky/Skyline + +### sbatch tempalte +```bash title="bigsky-skyline sbatch template" +#!/bin/bash +#SBATCH --job-name= +#SBATCH --export=ALL +#SBATCH --time=01-00:00:00 +#SBATCH --cpus-per-task=1 +#SBATCH --ntasks=1 +#SBATCH --mem=8g +#SBATCH --output=_%j.out +source ${dependencies} +weave run \ +-s /sequencing/root/dir \ +-o output_dir \ + +``` + +This above script can serve as a template to create an sbatch script for weave. Update the psuedo-variables in the script to suit your particular needs then execute using sbatch command: + +```bash +sbatch weave_script.sbatch +``` + +## Biowulf + +### sbatch tempalte +```bash title="biowulf sbatch template" +#!/bin/bash +#SBATCH --job-name= +#SBATCH --export=ALL +#SBATCH --time=01-00:00:00 +#SBATCH --cpus-per-task=1 +#SBATCH --ntasks=1 +#SBATCH --mem=8g +#SBATCH --output=_%j.out +module purge +module load snakemake singularity +weave run \ +-s /sequencing/root/dir \ +-o output_dir \ + +```