solida 0.8.3

NGS pipelines bootstrapper

SOLIDA is command-line solution that facilitate the reproducibility and portability of NGS pipelines. It can easily organize the deployment, the data management and the execution of a Snakemake based workflow.

Installation

You can install the latest stable version from PyPI

$ pip install solida

Prerequisites

To run Solida, you need Conda. To install it, see conda.io

Usage

To check version:

$ solida -v

To list all the pipelines enabled, digit

$ solida info

To check if both pipeline and profile are available, digit:

$ solida setup -l pipeline_label -p profile_label

Before to deploy a pipeline, you have to create a project profile:

$ solida setup -l pipeline_label -p profile_label --create-profile

Solida will create a yaml file named profile_label.yaml into ~/solida_profiles.

Edit the profile_label.yaml to match your environment settings.

After that, deploy the pipeline into localhost with:

$ solida setup -l pipeline_label -p profile_label --deploy

If you want to deploy the pipeline into a remote host, add these arguments:

$ solida setup -l pipeline_label -p profile_label --deploy --host remote_host --remote-user username --connection ssh

where:

–host is the hostname of the remote host

–remote-user is a username available in the remote host

–connection is the type of connection to use

Pay attention, remote_user have to be able to do ssh login into remote_host without password (SSH Key-Based Authentication)