Metadata-Version: 2.1
Name: solida
Version: 0.8.2
Summary: NGS pipelines bootstrapper
Home-page: https://bitbucket.org/biopipelines/solida
Author: Gianmauro Cuccuru
Author-email: gmauro@crs4.it
License: GPLv3
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 :: 2.7
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: ansible (>=2.4.0)
Requires-Dist: appdirs
Requires-Dist: comoda
Requires-Dist: gitpython

Solida
======
NGS pipelines bootstrapper

|build|

Installation
------------

You can install the latest stable version from PyPI

.. code:: console

    $ pip install solida


Prerequisites
-------------

To run Solida, you need Conda.
To install it, see `conda.io`_


Usage
-----

To check version:

.. code-block:: console

    $ solida -v

To list all the pipelines enabled, digit

.. code-block:: console

    $ solida info

To check if both pipeline and profile are available, digit:

.. code-block:: console

    $ solida setup -l pipeline_label -p profile_label

Before to deploy a pipeline, you have to create a project profile:

.. code-block:: console

    $ 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:

.. code-block:: console

    $ solida setup -l pipeline_label -p profile_label --deploy

If you want to deploy the pipeline into a remote host, add these
arguments:

.. code-block:: console

    $ 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)

.. _conda.io: https://conda.io/miniconda.html

.. |build| image:: https://travis-ci.org/gmauro/solida.svg?branch=master
   :target: https://travis-ci.org/gmauro/solida
   :alt: Continuous Integration

.. |license| image:: http://img.shields.io/badge/license-GPLv3-blue.svg
   :target: https://github.com/gmauro/solida/blob/master/LICENSE


