docs: improve docs

.gitignore

@@ -0,0 +1,10 @@
+# image build artifacts
+envs/*.sif
+
+# snakemake
+snakemake.log
+.snakemake/
+
+# vim swaps
+*.swp
+*.swo

Makefile

@@ -0,0 +1,11 @@
+MAX_CORES ?= 10
+# by default, we want to run all snakemake rules even if there are failures
+OB_CMD=ob run benchmark -k --local --task-timeout "4h"
+prepare_apptainer_env:
+	cd envs && ./build_singularity.sh
+run_with_apptainer_backend:
+	 ${OB_CMD} -b Clustering_singularity.yml --cores ${MAX_CORES}
+	 mv out out_apptainer
+run_with_conda_backend:
+	 ${OB_CMD} -b Clustering_conda.yml --cores ${MAX_CORES}
+	 mv out out_conda

README.md

@@ -3,8 +3,8 @@ A clustering example for omnibenchmark
 # How to run
 
 1. Install omnibenchmark using [our tutorial](https://omnibenchmark.org/tutorial/)
-2. Clone the benchmark definition / this repository with `git clone git@github.com:omnibenchmark/clustering_example.git`
-3. Move to the cloned repository `cd clustering_example`
+2. Clone the benchmark definition / this repository with `git clone https://github.com/omnibenchmark/clustering_example`
+3. Move into the cloned folder: `cd clustering_example`
 4. Run locally, somewhat in parallel `ob run benchmark -b CLUSTERING.YAML  --local --threads 6`. Choose `Clustering.yml` specification based on whether running it with conda, easybuild, apptainer, etc. [More details about the available backends](https://github.com/omnibenchmark/clustering_example/blob/main/envs/README.md).
 
 # Clustbench attribution

envs/build_singularity.sh

@@ -1,9 +1,5 @@
-#!/bin/bash
-
-sudo singularity build sklearn.sif sklearn_singularity.def
-
-sudo singularity build clustbench.sif clustbench_singularity.def
-
-sudo singularity build r.sif r_singularity.def
-
-sudo singularity build fcps.sif fcps_singularity.def
+#!/bin/sh
+singularity build sklearn.sif sklearn_singularity.def
+singularity build clustbench.sif clustbench_singularity.def
+singularity build r.sif r_singularity.def
+singularity build fcps.sif fcps_singularity.def