Merge pull request #31 from TurakhiaLab/documentation

Added contribution and troubleshooting steps

README.md

@@ -7,10 +7,11 @@
 
 [![License][license-badge]][license-link]
 [![Build Status](https://github.com/TurakhiaLab/ROADIES/actions/workflows/ci.yml/badge.svg)](https://github.com/TurakhiaLab/ROADIES/actions)
-[<img src="https://img.shields.io/badge/Made with-Snakemake-brightgreen.svg?logo=snakemake">](https://snakemake.readthedocs.io/en/v7.19.1/index.html)
+[<img src="https://img.shields.io/badge/Made with-Snakemake-green.svg?logo=snakemake">](https://snakemake.readthedocs.io/en/v7.19.1/index.html)
+[<img src="https://img.shields.io/badge/Install with-Biooconda-brightgreen.svg?logo=conda">](http://bioconda.github.io/recipes/roadies/README.html)
 [<img src="https://img.shields.io/badge/Install with-DockerHub-informational.svg?logo=Docker">](https://hub.docker.com/r/ang037/roadies)
 [<img src="https://img.shields.io/badge/Submitted to-bioRxiv-critical.svg?logo=LOGO">](https://www.biorxiv.org/content/10.1101/2024.05.27.596098v1)
-[<img src="https://img.shields.io/badge/DOI-10.5061/dryad.tht76hf73-brightgreen.svg?logo=LOGO">](https://doi.org/10.5061/dryad.tht76hf73)
+[<img src="https://img.shields.io/badge/DOI-10.5061/dryad.tht76hf73-yellowgreen.svg?logo=LOGO">](https://doi.org/10.5061/dryad.tht76hf73)
 [<img src="https://img.shields.io/badge/Watch it on-Youtube-FF0000.svg?logo=YouTube">](https://youtu.be/1sR741TvZnM?si=vVNAnonvzNEzrLKq)
 
 <div align="center">
@@ -59,7 +60,9 @@ Welcome to the official repository of ROADIES, a novel pipeline designed for phy
 
 To run ROADIES using Bioconda package, follow these steps:
 
-**Note:** You need to have conda installed in your system. To install and use conda in Ubuntu machine, execute the set of commands below:
+**Note:** You need to have conda installed in your system. Also make sure you have updated version of glibc in your system (`GLIBC >= 2.29`).
+
+To install and use conda in Ubuntu machine, execute the set of commands below:
 
 ```
 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
@@ -89,7 +92,7 @@ conda activate myenv
 conda install roadies
 ```
 
-All files of ROADIES along with dependencies will be found in `<conda_install_path>/miniconda3/envs/new_env/ROADIES`.
+All files of ROADIES along with dependencies will be found in `<conda_install_path>/miniconda3/envs/myenv/ROADIES`.
 
 ### <a name="dockerhub"></a> Using DockerHub
 
@@ -143,13 +146,14 @@ This will install and build all tools and dependencies. Once the setup is comple
 #### Required dependencies
 
 To run this script, ensure the following dependencies are installed:
-- Java Runtime Environment (version 1.7 or higher)
-- Python (version 3.9 or higher)
+- Java Runtime Environment (Version 1.7 or higher)
+- Python (Version 3.9 or higher)
 - `wget` and `unzip` commands
-- GCC (version 11.4 or higher)
+- GCC (Version 11.4 or higher)
 - cmake (Download here: https://cmake.org/download/)
 - Boost library (Download here: https://boostorg.jfrog.io/artifactory/main/release/1.82.0/source/)
 - zlib (Download here: http://www.zlib.net/)
+- GLIBC (Version 2.29 or higher)
 
 For Ubuntu, you can install these dependencies with: 
 
@@ -217,6 +221,10 @@ python run_roadies.py --cores 16 --mode fast
 
 <br>
 
+### For troubleshooting and contribution details, refer to [Wiki](https://turakhialab.github.io/ROADIES/)
+
+<br>
+
 ## <a name="citation"></a> Citing ROADIES
 
 If you use ROADIES in your research or publications, please cite the following paper:

docs/cite.md

@@ -0,0 +1,11 @@
+# Cite ROADIES
+
+If you use ROADIES in your research or publications, please cite the following paper:
+
+Gupta A, Mirarab S, Turakhia Y, (2024). Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES. _bioRxiv_. [https://www.biorxiv.org/content/10.1101/2024.05.27.596098v1](https://www.biorxiv.org/content/10.1101/2024.05.27.596098v1).
+
+## Accessing ROADIES output files
+
+The output files with the gene trees and species trees generated by ROADIES in the manuscript are deposited to [Dryad](https://datadryad.org/stash). To access it, please refer to the following:
+
+Gupta, Anshu; Mirarab, Siavash; Turakhia, Yatish (2024). Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES [Dataset]. Dryad. [https://doi.org/10.5061/dryad.tht76hf73](https://doi.org/10.5061/dryad.tht76hf73).

docs/contribution.md

@@ -0,0 +1,72 @@
+# Contributions
+
+Thank you for considering contributing to **ROADIES**! We value your input and want to make it as easy as possible to get involved. Whether you're reporting a bug, adding a feature, or improving documentation, this guide will help you understand how to contribute effectively.
+
+## Table of Contents
+- [How to Contribute](#how-to-contribute)
+    - [Reporting Bugs](#reporting-bugs)
+    - [Suggesting Features](#suggesting-features)
+    - [Documentation Update](#documentation-update)
+    - [Submitting Changes](#submitting-changes)
+- [Pull Request Guidelines](#pull-request-guidelines)
+- [License](#license)
+- [Contact Information](#contact-information)
+
+## How to Contribute
+
+### Reporting Bugs
+If you find a bug, please [open an issue](https://github.com/TurakhiaLab/ROADIES/issues) and include:
+
+- A clear description of the issue, including steps to reproduce it.
+- Screenshots or logs if applicable.
+
+### Suggesting Features
+We welcome feature requests! Please [open a new feature request issue](https://github.com/TurakhiaLab/ROADIES/issues) and include:
+
+- A clear description of the feature.
+- Use a label for the issue you created - `new feature request`.
+- Why it would be useful and how it fits with the project’s existing features.
+- Any alternatives you've considered.
+
+### Documentation Update
+If you want to suggest some updates/modifications in our documentation or, please [open a new documentation issue](https://github.com/TurakhiaLab/ROADIES/issues) and include:
+
+- Clear description of the modifications or suggested additions.
+- Use a label for the issue you created - `documentation`.
+
+
+### Submitting Changes
+1. Fork the repository.
+2. Create a new branch (`git checkout -b feature/your-feature`).
+3. Make your changes.
+4. Ensure your changes pass all tests. To check that, run the following command:
+
+```bash
+cd ROADIES
+python run_roadies.py --cores 16
+```
+After running this command, if you are able to successfully create the final species tree, the changes passed the test and its ready to be pushed to the forked repository. 
+
+5. Commit your changes (`git commit -m 'Add new feature'`).
+6. Push your changes to your fork (`git push origin feature/your-feature`).
+7. Create a pull request.
+
+Please keep your pull requests small and focused. Large pull requests are harder to review and can delay the process.
+
+## Pull Request Guidelines
+- Ensure the title is concise but descriptive.
+- Include a detailed description of what the pull request does.
+- Follow the [commit message guidelines](#https://github.com/TurakhiaLab/ROADIES/blob/main/.github/pull_request_template.md).
+- Link to any related issues or pull requests.
+
+## License
+
+By contributing, you agree that your contributions will be licensed under the [MIT License](https://github.com/TurakhiaLab/ROADIES/blob/main/LICENSE).
+
+## Contact Information
+
+For general inquiries and support, reach out to our team.
+
+Anshu Gupta - ang037 [at] ucsd [dot] edu
+
+Yatish Turakhia - yturakhia [at] ucsd [dot] edu