From 75141e62d32af976c565d4f7e4a3750e0e316c64 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= Date: Fri, 5 Jan 2024 10:14:14 +0100 Subject: [PATCH] Add disclaimer about containerized runs --- config/README.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/config/README.md b/config/README.md index 2f746c5..04e5570 100644 --- a/config/README.md +++ b/config/README.md @@ -171,3 +171,11 @@ provided that [Singularity](https://en.wikipedia.org/wiki/Singularity_(software) is available on the system. This eliminates the need for further conda package downloads and environment configuration. To do that, simply add the option `--use-singularity` to any of the previous commands. + +Using Singularity for running VIPERA in the Windows Subsystem for Linux (WSL) +may encounter errors due to the default file permissions configuration, which +conflicts with Snakemake's containerized conda environment activation mechanism. +Thus, running the containerized VIPERA workflow on the WSL is not advised. +Additionally, certain known issues arise when utilizing non-default temporary +directories. To address this issue, set the temporary directory to the default +before executing the workflow (e.g. `export TMPDIR=/tmp` in Linux machines).