From 3077b2afe8cb31e4f442550304dec22bc6c551f6 Mon Sep 17 00:00:00 2001 From: Mette Bentsen Date: Fri, 22 Mar 2019 11:44:27 +0100 Subject: [PATCH] Update README.md --- README.md | 18 ++---------------- 1 file changed, 2 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 8593e25..127f512 100644 --- a/README.md +++ b/README.md @@ -26,12 +26,10 @@ TOBIAS is written as a python package and can be quickly installed via pip: pip install tobias ``` -or directly from github into a conda environment using: +or directly from github using: ```bash $ git clone https://github.molgen.mpg.de/loosolab/TOBIAS $ cd TOBIAS -$ conda env create -f snakemake_pipeline/environments/tobias.yaml -$ conda activate TOBIAS_ENV $ python setup.py install ``` Please see the [installation](https://github.molgen.mpg.de/loosolab/TOBIAS/wiki/installation) page for more info. @@ -119,19 +117,7 @@ $ TOBIAS FormatMotifs --input test_data/example_motifs.txt --format pfm --task s Snakemake pipeline ------------ -You can run each TOBIAS tool independently or as part of a pipeline using the included snakemake workflow. To use the snakemake pipeline, make sure the included conda environments are installed: -``` -$ conda env create -f snakemake_pipeline/environments/tobias.yaml -$ conda env create -f snakemake_pipeline/environments/macs.yaml -``` - -You can use the example config (snakemake_pipeline/TOBIAS_example.config) or adjust to your own data by replacing the values for each key. Run using: -```bash -$ cd snakemake_pipeline -$ conda activate TOBIAS_ENV -$ snakemake --snakefile TOBIAS.snake --configfile TOBIAS_example.config --cores [number of cores] --keep-going -``` -For further info on setup, configfile and output, please consult the [wiki](https://github.molgen.mpg.de/loosolab/TOBIAS/wiki/snakemake-pipeline). +You can run each TOBIAS tool independently or as part of a pipeline. We provide a pre-set snakemake workflow which is found [here](https://github.molgen.mpg.de/loosolab/TOBIAS_snakemake). License ------------