From a1a0b924f59e9a8f14002067fde557bf0557115c Mon Sep 17 00:00:00 2001 From: Sam Horsfield Date: Thu, 27 Apr 2023 13:24:04 +0100 Subject: [PATCH] Adds instructions for singularity installation to docs --- docs/installation.rst | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/docs/installation.rst b/docs/installation.rst index dd38446..236a12e 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -13,7 +13,7 @@ We plan to get a MacOS version up and running in the future. Installing with Docker (recommended) ----------------------------------- -First, install (`Docker `_) for your OS. If running with WSL2, you should still download Docker Desktop for Windows. +First, install `Docker `_ for your OS. If running with WSL2, you should still download Docker Desktop for Windows. To use the latest image, run:: @@ -35,6 +35,20 @@ To run ggCaller from a local Docker build, run:: cd test && docker run --rm -it -v $(pwd):/workdir ggc_env:latest ggcaller --refs pneumo_CL_group2.txt +Installing with singularity +----------------------------------- + +If you encounter permissions issues using Docker, you can download the singularity image from `Zenodo `_ + +Once downloaded, set up the singularity container using:: + + singularity shell --writable .sif + +Once loaded, add the conda bin directory to your path variable and run ggCaller as normal:: + + PATH=$PATH:/opt/conda/bin + ggcaller --refs input.txt --out output_path + Installing with conda -----------------------------------