Installation

We have run BSATOS on Linux (CentOS, Ubuntu) and Mac (El Capitan v10.11.6) system .

Installation:

1) Run in Conda environment

1. Download the latest BSATOS:

   git clone https://github.com/maypoleflyn/BSATOS.git

2. Find the yml file in the folder and run:

   conda env create -f bsatos.yml

   conda activate bsatos

3. add BSATOS in the path

   chmod 777 /path/to/BSATOS/scripts/*

   chmod 777 /path/to/BSATOS/bsatos

   export PATH=$PATH:/path/to/BSATOS/

   export PATH=$PATH:/path/to/BSATOS/scripts/

   R CMD INSTALL /path/to/BSATOS/scripts/dependancy/modeest_2.1.tar.gz

2) Run in Docker

We distribute BSATOS as a convenient dockerfile, which can be downloaded from dockerhub:

docker pull flynshen/bsatos:latest

The BSATOS container can be run using:

docker run -i -t flynshen/bsatos /bin/bash

Once the container is started, BSATOS can be run with:

bsatos

which will give a list of possible commands and a command line guide. All the steps of the pipeline can be manually run one after the other, but we recommend to launch the full pipeline with:

bsatos all

which will create a bash script with all the commands of the pipeline that can then be invoked to run the whole analysis process.

We recommend to run the BSATOS container with the following command:

docker run --rm --volume $PWD:/BSATOS --workdir /BSATOS -i -t flynshen/bsatos /bin/bash

where local_folder is a folder in the local machine that contains all the data. This folder would be mounted, within the BSATOS container, in /BSATOS/data and the owner of the data would be the local user.