NGS pipelines bootstrapper
Project description
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
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)
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