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        "author": "Gianmauro Cuccuru",
        "author_email": "gmauro@crs4.it",
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            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# Solida [![Build Status](https://travis-ci.org/gmauro/solida.svg?branch=master)](https://travis-ci.org/gmauro/solida)\nSOLIDA 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.\n\n## Installation\n\nYou can install the latest stable version from PyPI\n```bash\npip install solida\n```\n\n## Requirements\n\nTo run Solida, Conda must be present in your computer.    \nTo install it, see [https://conda.io/miniconda.html](https://conda.io/miniconda.html) \n\n## Usage\n\nTo check version:\n```bash\nsolida -v\n```\n\nTo list all the pipelines enabled, digit\n```bash\nsolida info\n```\n\nTo check if both pipeline and profile are available, digit:\n```bash\nsolida setup -l pipeline_label -p profile_label\n```\n\nBefore to deploy a pipeline, you have to create a project profile:\n```bash\nsolida setup -l pipeline_label -p profile_label --create-profile \n```\nSolida will create a yaml file named _profile_label.yaml_ into _~/solida_profiles_  \nEdit the _profile_label.yaml_ to match your environment settings.\n\nAfter that, deploy the pipeline into localhost with:\n```bash\nsolida setup -l pipeline_label -p profile_label --deploy \n```\nIf you want to deploy the pipeline into a remote host, add these \narguments:\n```bash\nsolida setup -l pipeline_label -p profile_label --deploy --host remote_host \n--remote-user username --connection ssh\n```\nwhere:  \n_--host_ is the hostname of the remote host  \n_--remote-user_ is a username available in the remote host  \n_--connection_ is the type of connection to use  \n\nPay attention, _remote_user_ have to be able to do ssh login into _remote_host_ \nwithout password (SSH Key-Based Authentication)\n\n### Script to execute the workflow\nSolida provides a bash script, _**run.project.sh**_, to facilitate the \nworkflow execution.  \n\n```\nrun.project.sh [-h] [-s Snakefile] -c FILENAME [-w DIR] [-p \"parameters\"] --script to execute a snakemake workflow\n\nwhere:\n    -h  show this help text\n    -s  path to a Snakefile different from the default one (Snakefile).\n    -c  path to the snakemake's configuration file.\n    -w  is the project's workdir label. Default is current timestamp.\n    -p  snakemake parameters as \"--rerun-incomplete --dryrun --keep-going --restart-time\"\n```\nUse _-s_ to specify a different Snakefile.  \n\nIf you don't give the script a workdir label (_-w_), a directory with the current \ntimestamp as label will be created and used to collect results into.\n\nOption _-c_ is mandatory and have to be the path to the snakemake's configuration file.\n\nOption _-p_ permit to provide the script all the snakemake parameters (don't \nforget to encapsulate them with \"\"\").\n\n\n",
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        "keywords": "NGS,pipeline deployment,bioinformatics",
        "license": "GPLv3",
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        "name": "solida",
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