Alignment Extraction

Installation

Cloning the repository

Traverse to the desired path on your file system, then clone the repository and move into it with:

git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_group/pipelines/rhea.git
cd rhea

Installing Conda

Workflow dependencies can be conveniently installed with the [Conda][conda] package manager. We recommend that you install [Miniconda][miniconda-installation] for your system (Linux). Be sure to select Python 3 option. The workflow was built and tested with miniconda 4.7.12. Other versions are not guaranteed to work as expected.

Installing dependencies

For improved reproducibility and reusability of the workflow, each individual step of the workflow runs in its own [Singularity][singularity] container. As a consequence, running this workflow has very few individual dependencies. It does, however, require Singularity to be installed on the system running the workflow. As the functional installation of Singularity requires root privileges, and Conda currently only provides Singularity for Linux architectures, the installation instructions are slightly different depending on your system/setup:

For most users

If you do not have root privileges on the machine you want to run the workflow on or if you do not have a Linux machine, please [install Singularity][singularity-install] separately and in privileged mode, depending on your system. You may have to ask an authorized person (e.g., a systems administrator) to do that. This will almost certainly be required if you want to run the workflow on a high-performance computing (HPC) cluster. We have successfully tested the workflow with the following Singularity versions:

v2.4.5
v2.6.2
v3.5.2

After installing Singularity, install the remaining dependencies with:

conda env create -f install/environment.yml

As root user on Linux

If you have a Linux machine, as well as root privileges, (e.g., if you plan to run the workflow on your own computer), you can execute the following command to include Singularity in the Conda environment:

conda env create -f install/environment.root.yml

Activate environment

Activate the Conda environment with:

conda activate rhea

Installing non-essential dependencies

Most tests have additional dependencies. If you are planning to run tests, you will need to install these by executing the following command in your active Conda environment:

conda env update -f install/environment.dev.yml

Testing the installation

We have prepared several tests to check the integrity of the workflow, its components and non-essential processing scripts. These can be found in subdirectories of the tests/ directory.

Note that for this and other tests to complete without issues, additional dependencies need to be installed.

Preparing annotations

Select organism (If the organism is missing you can use as template on of the existing ones)

cd AlignmentExtraction/prepare_annotation/snakemake/<prefered organism>

Fill in the config.yaml

Create a dag (optional)

bash create_snakemake_flowchart.sh

Run the pipeline locally

bash run_on_local.sh

or in a cluster (tested with slurm)

bash run_on_cluster.sh

Generating mirzag input files

Once the previous step is complete (prepare_annotation) go to

../../runs/<prefared organism>/snakemake/

fgypas / AlignmentExtraction