Instalation and setup

Download the source code

git clone https://github.com/vertical-space/ALISEQ
git clone https://github.com/secastel/allelecounter.git ALISEQ/allelecounter

export SRC_DIR=`pwd`
conda env create -f ALISEQ/envs/aliseq.yaml -p ${SRC_DIR}/ALISEQ
source activate aliseq

export TEST_DIR=testdirectory # or whatever you want to call your working directory

mkdir ${TEST_DIR}
cp ALISEQ/data/aliseq_params.txt ${TEST_DIR}
cp ALISEQ/data/simulation_params.txt ${TEST_DIR}
cp ALISEQ/data/targets.txt ${TEST_DIR}
cd ${TEST_DIR}

Test if it’s working

bash ../ALISEQ/aliseq.sh

Note: The first time you run this it will take a while to download the dependencies