From a62154ca9c57826cf163599ec5b27b8ac40cbd25 Mon Sep 17 00:00:00 2001 From: renewiegandt Date: Thu, 6 Dec 2018 10:34:44 +0100 Subject: [PATCH] Update README.md --- README.md | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 6431022..f36beca 100644 --- a/README.md +++ b/README.md @@ -10,13 +10,23 @@ De novo motif discovery and evaluation based on footprints identified by TOBIAS ## Installation Start with installing all dependencies listed above. Download all files from the [GitHub repository](https://github.molgen.mpg.de/loosolab/masterJLU2018). -The Nextflow-script needs a conda enviroment to run. To create this enviroment you need the yml-file from the repository. +The Nextflow-script needs a conda enviroment to run. Nextflow can create the needed enviroment from the given yaml-file. +On some systems Nrxtflow exits the run with following error: +``` +Caused by: + Failed to create Conda environment + command: conda env create --prefix --file env.yml + status : 143 + message: +``` +If this error occurs you have to create the enviroment before starting the pipeline. +To create this enviroment you need the yml-file from the repository. Run the following commands to create the enviroment: ```console path=[Path to given masterenv.yml file] conda env create --name masterenv -f=$path -source activate masterenv ``` +When the enviroment is created, set the variable 'path_env' in the configuration file as the path to it. ## Quick Start ```console