Merge pull request #20 from B-UMMI/update_docs

Update docs to include Bioconda installation option

Author: cimendes

README.md

@@ -6,6 +6,9 @@
 
 [![Nextflow](https://img.shields.io/badge/nextflow-DLS2-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.01.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
+[![Anaconda-Server Badge](https://anaconda.org/bioconda/LMAS/badges/installer/conda.svg)](https://bioconda.github.io/recipes/lmas/README.html) 
+[![Anaconda-Server Badge](https://anaconda.org/bioconda/LMAS/badges/downloads.svg)](https://anaconda.org/bioconda/LMAS)
+
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![run with shifter](https://img.shields.io/badge/run%20with-shifter-lightgrey?labelColor=000000)](https://github.com/NERSC/shifter/)
@@ -32,19 +35,7 @@ The *de novo* assembly of raw sequence data is a key process when analysing data
 
 ## Instalation
 
-Before installing LMAS, a few dependencies must be installed in your system:
-
-
-### Nextflow
-
-Nextflow (version 20.01.0 or higher) can be used on any POSIX compatible system (Linux, OS X, etc). It requires BASH and 
-Java 8 (or higher) to be installed. More instructions are available [here](https://www.nextflow.io/docs/latest/getstarted.html).
-
-
-### Container Engine
-
-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:
+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:
 
 * [Docker](https://www.nextflow.io/docs/latest/docker.html),
 * [Singularity](https://www.nextflow.io/docs/latest/singularity.html),
@@ -53,23 +44,37 @@ installed. The container engines available are the ones supported by Nextflow:
 If you already have any one of these installed, you are good to go as the provided docker containers are compatible 
 with all engines available. If not, you’ll need to install one.
 
+### Conda
 
-### Clone LMAS
+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:
 
-You can clone this repository with `git clone [email protected]:cimendes/LMAS.git`, and all files will be in your local machine.
+```bash
+conda install -c bioconda lmas
+```
+
+### Manual installation
+
+To install LMAS manually you'll first have to install nextflow. 
+#### Nextflow
+
+Nextflow (version 20.01.0 or higher) can be used on any POSIX compatible system (Linux, OS X, etc). It requires BASH and 
+Java 8 (or higher) to be installed. More instructions are available [here](https://www.nextflow.io/docs/latest/getstarted.html).
 
+#### Clone LMAS
+
+You can clone this repository with `git clone [email protected]:cimendes/LMAS.git`, and all files will be in your local machine.
 
 ## Running LMAS
 
 To run LMAS you can simply call it with:
 
-    ./LMAS <options>
+   LMAS <options>
 
 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.
 
 Alternatively you can call LMAS directly with Nextflow:
 
-      nextflow run main.nf <options>
+   nextflow run main.nf <options>
 
 To use LMAS the following options are available:
 
@@ -245,11 +250,11 @@ Simulated samples of the evenly and log distributed reads, with and without erro
 
 After downloading the data you can simply run LMAS, with default parameters, with the following command:
 
-      ./LMAS -profile docker
+      LMAS -profile docker
 
 or
 
-      nextflow run LMAS.nf -profile docker
+      nextflow run main.nf -profile docker
 
 ## Citation and Contacts
 

docs/getting_started/installation.rst

@@ -1,31 +1,11 @@
 Installation
 ============
 
-LMAS can be installed through Github (https://github.com/cimendes/LMAS).
-It requires a `Nextflow <https://www.nextflow.io/>`_ installation (version ≥ 21.04.1) 
-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/>`_, 
-being a container engine required. 
-
-Nextflow allows integration with multiple alternatives, such as `Shifter <https://github.com/NERSC/shifter/>`_ or 
-`Singularity <https://singularity.hpcng.org/>`_, so a particular one isn’t required. 
+Container engine
+----------------------
 
-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
-and the python templates is performed with `GitHub Actions <https://github.com/features/actions>`_ and `pytest <https://docs.pytest.org/en/6.2.x/>`_. 
-
-Below it's a step by step guide on how to install LMAS and all its dependencies.
-
-Step 1. Nextflow
------------------
-
-`Nextflow <https://www.nextflow.io/>`_ (version 20.01.0 or higher) can be used on any POSIX compatible system (Linux, OS X, etc). 
-It requires BASH and Java 8 (or higher) to be installed. 
-
-.. important::
-
-    Instructions on how to install Nextflow are available `here <https://www.nextflow.io/docs/latest/getstarted.html>`_
-
-Step 2. Container engine
--------------------------
+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.
 
 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:
@@ -37,7 +17,6 @@ installed. The container engines available are the ones supported by Nextflow:
 If you already have any one of these installed, you are good to go as the provided docker containers are compatible 
 with all engines available. If not, you’ll need to install one.
 
-
 Singularity
 :::::::::::
 
@@ -61,8 +40,46 @@ https://www.docker.com/community-edition#/download.
 To run docker as a non-root user, you'll need to follow the instructions
 on the website: https://docs.docker.com/install/linux/linux-postinstall/#manage-docker-as-a-non-root-user
 
-Step 3. Clone LMAS
--------------------
+
+Installation through conda
+----------------------------
+
+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:
+
+.. code-block:: bash
+    
+    conda install -c bioconda lmas
+
+Manual installation
+--------------------------
+
+LMAS can be installed through Github (https://github.com/cimendes/LMAS).
+It requires a `Nextflow <https://www.nextflow.io/>`_ installation (version ≥ 21.04.1) 
+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/>`_, 
+being a container engine required. 
+
+Nextflow allows integration with multiple alternatives, such as `Shifter <https://github.com/NERSC/shifter/>`_ or 
+`Singularity <https://singularity.hpcng.org/>`_, so a particular one isn’t required. 
+
+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
+and the python templates is performed with `GitHub Actions <https://github.com/features/actions>`_ and `pytest <https://docs.pytest.org/en/6.2.x/>`_. 
+
+Below it's a step by step guide on how to install LMAS and all its dependencies.
+
+Step 1. Nextflow
+^^^^^^^^^^^^^^^^^
+
+`Nextflow <https://www.nextflow.io/>`_ (version 20.01.0 or higher) can be used on any POSIX compatible system (Linux, OS X, etc). 
+It requires BASH and Java 8 (or higher) to be installed. 
+
+.. important::
+
+    Instructions on how to install Nextflow are available `here <https://www.nextflow.io/docs/latest/getstarted.html>`_
+
+Step 2. Clone LMAS
+^^^^^^^^^^^^^^^^^^^^^^^^
 
 You can clone this repository with git.