From 86af84ac48048cecaa12cda1217834ea659faa2a Mon Sep 17 00:00:00 2001 From: Erik Storrs Date: Mon, 13 Nov 2023 12:54:40 -0600 Subject: [PATCH] Update README.md --- README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.md b/README.md index f15ae11..27bce3a 100644 --- a/README.md +++ b/README.md @@ -37,6 +37,12 @@ The tutorial/example notebook you can use to generate the bsub commands that run I would recommend putting your run directory inside `/scratch1` as tools tend to run faster in scratch1 than in storage1. +Compute1 messes with the PATH variable in docker files, causing some libraries not to be found. To fix this, before running bsub, you will need to run the following command: + +```bash +export PATH="/miniconda/envs/ancestry/bin:$PATH" +``` + NOTE: you will likely need to make some small changes to the example notebook to specify input/output files, etc. ## Output format