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NGS pipelines bootstrapper

Project description

Solida Build Status

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 must be present in your computer.
To install it, see https://conda.io/miniconda.html

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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