From 63da22abe9269de5cc87f581ad9aeeee6e175715 Mon Sep 17 00:00:00 2001 From: April Shen <ashen@ebi.ac.uk> Date: Tue, 2 Jan 2024 10:50:21 +0000 Subject: [PATCH] add conda installation to readme --- README.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/README.md b/README.md index c785927c..46f97b4a 100644 --- a/README.md +++ b/README.md @@ -52,6 +52,19 @@ nextflow run ${CODE_ROOT}/pipelines/annotation_pipeline.nf \ --mappings ${LATEST_MAPPINGS} ``` +### Conda + +You can also install CMAT using Conda. +For example the following installs CMAT in a new environment called `cmat`, activates the environment, and prints usage: +```bash +conda create -n cmat -c conda-forge -c bioconda cmat +conda activate cmat +cmat +``` + +Note that with conda installation you can't invoke the pipelines directly via Nextflow, so you will need to use the corresponding `cmat` commands - e.g. `cmat annotate` instead of `nextflow run annotation_pipeline.nf`. +All the same command line options apply. + ## Run CMAT includes a main annotation pipeline (which also performs consequence and gene mapping), as well as two pipelines to help manage trait mapping curation.