Installation¶
User installation¶
Assemblerflow is available as a bioconda package, which already comes with nextflow:
conda install assemblerflow
Alternatively, you can install only Assemblerflow, via pip:
pip install assemblerflow
You will also need a container engine (see Container engine below)
Container engine¶
All components of assemblerflow are executed in docker containers, which means that you’ll need to have a container engine installed. The container engines available are the ones supported by Nextflow:
- Docker,
- Singularity
- Shifter (undocumented)
If you already have any one of these installed, you are good to go. If not, you’ll need to install one. We recommend singularity because it does not require the processes to run on a separate root daemon.
Singularity¶
Singularity is available as a bioconda package. Simply install it, and it’s ready to use:
conda install singularity
Docker¶
Docker can be installed following the instructions on the website: https://www.docker.com/community-edition#/download. To run docker as anon-root user, you’ll need to following the instructions on the website: https://docs.docker.com/install/linux/linux-postinstall/#manage-docker-as-a-non-root-user
Developer installation¶
If you are looking to contribute to assemblerflow or simply interested in tweaking it, clone the github repository and its submodule and then run setup.py:
git clone https://github.com/ODiogoSilva/assemblerflow.git
cd assemblerflow
git submodule update --init --recursive
python3 setup.py install