Install the Client from Command Line

A pre-requisite is to have the samtools package installed, which is used to retrieve BAM header information. To read JSON/JSONL outputs in a friendly manner, we also suggest installing the jq package.

sudo apt install samtools
sudo apt install jq

Once samtools is installed, clone the repository:

git clone https://github.com/icgc-argo/seq-tools.git

Using pip, install seq-tools:

cd seq-tools
pip3 install -r requirements.txt  # installs Python dependencies
pip3 install . # installs seq-tools```

You can verify that the installation worked by checking the version:

seq-tools -v

To update the client to the latest version, pull the latest version of the repository and run:

git pull
cd seq-tools
pip3 install .