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Merge pull request #20 from B-UMMI/update_docs
Update docs to include Bioconda installation option
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README.md

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[![Nextflow](https://img.shields.io/badge/nextflow-DLS2-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
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[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.01.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
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[![Anaconda-Server Badge](https://anaconda.org/bioconda/LMAS/badges/installer/conda.svg)](https://bioconda.github.io/recipes/lmas/README.html)
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[![Anaconda-Server Badge](https://anaconda.org/bioconda/LMAS/badges/downloads.svg)](https://anaconda.org/bioconda/LMAS)
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[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
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[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
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[![run with shifter](https://img.shields.io/badge/run%20with-shifter-lightgrey?labelColor=000000)](https://github.com/NERSC/shifter/)
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## Instalation
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Before installing LMAS, a few dependencies must be installed in your system:
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### Nextflow
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Nextflow (version 20.01.0 or higher) can be used on any POSIX compatible system (Linux, OS X, etc). It requires BASH and
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Java 8 (or higher) to be installed. More instructions are available [here](https://www.nextflow.io/docs/latest/getstarted.html).
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### Container Engine
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All components of LMAS are executed in docker containers, which means that you’ll need to have a container engine
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installed. The container engines available are the ones supported by Nextflow:
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All components of LMAS are executed in docker containers, which means that you’ll need to have a container engine installed. The container engines available are the ones supported by Nextflow:
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* [Docker](https://www.nextflow.io/docs/latest/docker.html),
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* [Singularity](https://www.nextflow.io/docs/latest/singularity.html),
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If you already have any one of these installed, you are good to go as the provided docker containers are compatible
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with all engines available. If not, you’ll need to install one.
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### Conda
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### Clone LMAS
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LMAS can be easily installed through [Conda](https://conda.io/en/latest/), an open source package management system and environment management system that runs on Windows, macOS and Linux. After its installation, LMAS is available on [Bioconda](https://anaconda.org/bioconda/LMAS) and can be easily installed with:
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You can clone this repository with `git clone [email protected]:cimendes/LMAS.git`, and all files will be in your local machine.
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```bash
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conda install -c bioconda lmas
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```
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### Manual installation
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To install LMAS manually you'll first have to install nextflow.
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#### Nextflow
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Nextflow (version 20.01.0 or higher) can be used on any POSIX compatible system (Linux, OS X, etc). It requires BASH and
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Java 8 (or higher) to be installed. More instructions are available [here](https://www.nextflow.io/docs/latest/getstarted.html).
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#### Clone LMAS
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You can clone this repository with `git clone [email protected]:cimendes/LMAS.git`, and all files will be in your local machine.
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## Running LMAS
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To run LMAS you can simply call it with:
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./LMAS <options>
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LMAS <options>
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If no option or `--help` is provided, LMAS will display its help message. Otherwise, the `--fastq` and `--reference` options are mandatory. By default they are set to `'data/fastq/*_{1,2}.*'` and `'data/reference/*.fasta'` respectively.
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Alternatively you can call LMAS directly with Nextflow:
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nextflow run main.nf <options>
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nextflow run main.nf <options>
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To use LMAS the following options are available:
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After downloading the data you can simply run LMAS, with default parameters, with the following command:
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./LMAS -profile docker
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LMAS -profile docker
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or
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nextflow run LMAS.nf -profile docker
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nextflow run main.nf -profile docker
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## Citation and Contacts
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docs/getting_started/installation.rst

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Installation
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============
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LMAS can be installed through Github (https://github.com/cimendes/LMAS).
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It requires a `Nextflow <https://www.nextflow.io/>`_ installation (version ≥ 21.04.1)
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and can be used on any POSIX compatible system (Linux, OS X, etc). All components of LMAS are executed in `Docker containers <https://www.docker.com/>`_,
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being a container engine required.
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Nextflow allows integration with multiple alternatives, such as `Shifter <https://github.com/NERSC/shifter/>`_ or
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`Singularity <https://singularity.hpcng.org/>`_, so a particular one isn’t required.
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Container engine
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----------------------
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To ensure the robustness of LMAS workflow and the custom python code for the quality assessment of assemblies, **continuous integration** of both the main workflow
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and the python templates is performed with `GitHub Actions <https://github.com/features/actions>`_ and `pytest <https://docs.pytest.org/en/6.2.x/>`_.
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Below it's a step by step guide on how to install LMAS and all its dependencies.
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Step 1. Nextflow
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-----------------
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`Nextflow <https://www.nextflow.io/>`_ (version 20.01.0 or higher) can be used on any POSIX compatible system (Linux, OS X, etc).
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It requires BASH and Java 8 (or higher) to be installed.
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.. important::
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Instructions on how to install Nextflow are available `here <https://www.nextflow.io/docs/latest/getstarted.html>`_
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Step 2. Container engine
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-------------------------
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All components of LMAS are executed in docker containers, which means that you’ll need to have a container engine installed.
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The container engines available are the ones supported by Nextflow.
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All components of LMAS are executed in docker containers, which means that you’ll need to have a container engine
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installed. The container engines available are the ones supported by Nextflow:
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If you already have any one of these installed, you are good to go as the provided docker containers are compatible
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with all engines available. If not, you’ll need to install one.
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Singularity
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:::::::::::
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To run docker as a non-root user, you'll need to follow the instructions
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on the website: https://docs.docker.com/install/linux/linux-postinstall/#manage-docker-as-a-non-root-user
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Step 3. Clone LMAS
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-------------------
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Installation through conda
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----------------------------
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LMAS can be easily installed through `Conda<https://conda.io/en/latest/>`_, an open source package management
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system and environment management system that runs on Windows, macOS and Linux.
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After its installation, LMAS is available on `Bioconda<https://anaconda.org/bioconda/LMAS>`_ and can be easily installed with:
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.. code-block:: bash
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conda install -c bioconda lmas
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Manual installation
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--------------------------
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LMAS can be installed through Github (https://github.com/cimendes/LMAS).
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It requires a `Nextflow <https://www.nextflow.io/>`_ installation (version ≥ 21.04.1)
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and can be used on any POSIX compatible system (Linux, OS X, etc). All components of LMAS are executed in `Docker containers <https://www.docker.com/>`_,
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being a container engine required.
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Nextflow allows integration with multiple alternatives, such as `Shifter <https://github.com/NERSC/shifter/>`_ or
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`Singularity <https://singularity.hpcng.org/>`_, so a particular one isn’t required.
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To ensure the robustness of LMAS workflow and the custom python code for the quality assessment of assemblies, **continuous integration** of both the main workflow
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and the python templates is performed with `GitHub Actions <https://github.com/features/actions>`_ and `pytest <https://docs.pytest.org/en/6.2.x/>`_.
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Below it's a step by step guide on how to install LMAS and all its dependencies.
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Step 1. Nextflow
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^^^^^^^^^^^^^^^^^
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`Nextflow <https://www.nextflow.io/>`_ (version 20.01.0 or higher) can be used on any POSIX compatible system (Linux, OS X, etc).
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It requires BASH and Java 8 (or higher) to be installed.
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.. important::
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Instructions on how to install Nextflow are available `here <https://www.nextflow.io/docs/latest/getstarted.html>`_
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Step 2. Clone LMAS
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^^^^^^^^^^^^^^^^^^^^^^^^
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You can clone this repository with git.
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