From 91593c913f436c7d2396d5f8cff70bf5b990e72e Mon Sep 17 00:00:00 2001 From: bio-la Date: Thu, 31 Aug 2023 18:19:56 +0200 Subject: [PATCH] adding conda info --- docs/install.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/install.md b/docs/install.md index 05ea94e4..64df7c00 100644 --- a/docs/install.md +++ b/docs/install.md @@ -155,9 +155,11 @@ If using conda environments, you can use one single big environment (the instruc The environment (s) should be specified in the .cgat.yml global configuration file or in each of the single workflows pipeline.yml configuration files and it will be picked up by the pipeline as the default environment. Please note that if you specify the conda environment in the workflows configuration file this will be the first choice to run the pipeline. +On some machines, you may find that `panpipes` is not picking up the correct conda env even if launching the command from a shell where this environment is active. +This is normal conda behaviour and documented [here](https://github.com/conda/conda/issues/9392#issuecomment-1291041085). +To let the pipeline pick up the right enviornment, run `conda config --set auto_activate_base false` - -If no environment is specified, the default behaviour of the pipeline is to inherit environment variables from the node where the pipeline is run. However there have been reported issues on SLURM clusters where this was not the default behaviour. +(or add `auto_activate_base: false` to your .condarc file) We recommend to add the conda environment param in the .cgat.yml file or in each of the pipeline.yml independently.