Metadata-Version: 2.1
Name: solida
Version: 0.9.7.1
Summary: NGS pipelines bootstrapper
Home-page: https://github.com/solida-core/solida
Author: Gianmauro Cuccuru
Author-email: gmauro@gmail.com
License: GPLv3
Description: # SOLIDA 
        [![Build Status](https://travis-ci.org/solida-core/solida.svg?branch=master)](https://travis-ci.org/solida-core/solida) 
        [![PyPI version](https://img.shields.io/pypi/v/solida.svg)](https://badge.fury.io/py/solida)
        
        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
        ```bash
        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](https://conda.io/miniconda.html) 
        To install Mamba, see [https://github.com/mamba-org/mamba](https://github.com/mamba-org/mamba)
        ```bash
        conda install -c conda-forge mamba```
        
        
        ## Usage
        
        To check version:
        ```bash
        solida -v
        ```
        
        To list all the pipelines enabled, digit
        ```bash
        solida info
        ```
        
        To check if both pipeline and profile are available, digit:
        ```bash
        solida setup -l pipeline_label -p profile_label
        ```
        
        Before to deploy a pipeline, you have to create a project profile:
        ```bash
        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:
        ```bash
        solida setup -l pipeline_label -p profile_label --deploy 
        ```
        If you want to deploy the pipeline into a remote host, add these 
        arguments:
        ```bash
        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 """).
        
Keywords: NGS,pipeline deployment,bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
