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NGS pipelines bootstrapper

Project description

SOLIDA

Build Status PyPI version

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

Requirements

To run Solida, Conda e Mamba must be presents in your computer.
To install Conda, see https://conda.io/miniconda.html To install Mamba, see https://github.com/mamba-org/mamba

conda install -c conda-forge mamba

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)

Script to execute the workflow

Solida provides a bash script, run.project.sh, to facilitate the workflow execution.

run.project.sh [-h] [-s Snakefile] -c FILENAME [-w DIR] [-p "parameters"] --script to execute a snakemake workflow

where:
    -h  show this help text
    -s  path to a Snakefile different from the default one (Snakefile).
    -c  path to the snakemake's configuration file.
    -w  is the project's workdir label. Default is current timestamp.
    -p  snakemake parameters as "--rerun-incomplete --dryrun --keep-going --restart-time"

Use -s to specify a different Snakefile.

If you don't give the script a workdir label (-w), a directory with the current timestamp as label will be created and used to collect results into.

Option -c is mandatory and have to be the path to the snakemake's configuration file.

Option -p permit to provide the script all the snakemake parameters (don't forget to encapsulate them with """).

Project details


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