Update README.md

README.md

@@ -1 +1,18 @@
-# 2021-whatsthatcell-analysis-Michael
+# Active learning benchmarking
+
+To reproduce the analysis in this repository and the associated paper follow these steps:
+
+1. Install `pipenv` using `pip install pipenv`
+2. Clone this repository `git clone [email protected]:camlab-bioml/active-learning-benchmarking.git`
+3. Move into the folder that was created as part of the previous step: `cd active-learning-benchmarking`
+4. Install the environment required for this analysis to work using `pipenv install`
+5. Create a snakemake profile by following these instructions: https://github.com/Snakemake-Profiles/slurm
+6. Inside the root directory of this repository run the following commands
+```
+module load singularity
+snakemake --profile [your_snakemake_profile] -j [n_jobs] --rerun-incomplete
+```
+
+where
+- [your_snakemake_profile] is the name of the snakemake profile you generated in step 5
+- [n_jobs] is the total number of jobs you would like to be submitted at a time