0.0.6

Author: John Major

ISSUES.md

@@ -2,6 +2,7 @@
 
 
 1. Change job names to be meaningful.
-2. Make `--comment` easy to pass through from config.
+2. Make `--comment` easy to pass through from config, ie with --default-resources comment='my-comment'
 3. Make random `slurm` flags easier to pass through from config, esp for globals.
-4. re-review the core plugin code, consider what can be added to make use of the novel aspects of pcluster which are not in the vanilla slurm plugin.
+4. re-review the core plugin code, consider what can be added to make use of the novel aspects of pcluster which are not in the vanilla slurm plugin.
+5. This is optimized to minimally run, this has not been heavily tuned for heavy and large compute environments.  It might be OK, but this is not known to be the case.

README.md

@@ -1,4 +1,4 @@
-# Snakemake executor plugin: pcluster-slurm v_0.0.4_
+# Snakemake executor plugin: pcluster-slurm v_0.0.6_
 
 # Snakemake Executor Plugins (generally)
 [Snakemake plugin catalog docs](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor).
@@ -22,5 +22,12 @@ _from an environment with snakemake and pip installed_
 pip install snakemake-executor-plugin-pcluster-slurm
 ```
 
+# Example Usage [daylily cluster headnode](https://github.com/Daylily-Informatics/daylily)
+```bash
+mkdir -p /fsx/resources/environments/containers/ubuntu/cache/
+export SNAKEMAKE_OUTPUT_CACHE=/fsx/resources/environments/containers/ubuntu/cache/
+snakemake --use-conda --use-singularity -j 10  --singularity-prefix /fsx/resources/environments/containers/ubuntu/ip-10-0-0-240/ --singularity-args "  -B /tmp:/tmp -B /fsx:/fsx  -B /home/$USER:/home/$USER -B $PWD/:$PWD" --conda-prefix /fsx/resources/environments/containers/ubuntu/ip-10-0-0-240/ --executor pcluster-slurm --default-resources slurm_partition='i64,i128,i192' --cache  --verbose
+```
+
 # More Documentation Pending For:
 ## How slurm uses `--comment` to tag resources created by the autoscaling cluster to tracke and mnage budgets.

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "snakemake-executor-plugin-pcluster-slurm"
-version = "0.0.4"
+version = "0.0.6"
 description = "A Snakemake executor plugin for submitting jobs to an AWS Parallel Cluster (pcluster) SLURM cluster."
 authors = [
     "John Major <john@daylilyinformatics.com>",