Merge pull request #46 from TurakhiaLab/package_updates

Package updates

Author: ang037

README.md

@@ -10,7 +10,7 @@
 [<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/Published in-PNAS-informational.svg?logo=LOGO">](https://doi.org/10.1073/pnas.2500553122)
 [<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)
 
@@ -97,7 +97,7 @@ conda install roadies
 5. Locate the installed files:
 
 ``` 
-cd $HOME/miniconda3/envs/roadies_env/ROADIES
+cd $CONDA_PREFIX/envs/roadies_env/ROADIES
 
 ```
 
@@ -256,7 +256,7 @@ The output species tree (unrooted) in Newick format will be saved as `roadies.nw
 
 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).
+A. Gupta, S. Mirarab, & Y. Turakhia, Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES, Proc. Natl. Acad. Sci. U.S.A. 122 (19) e2500553122, [https://doi.org/10.1073/pnas.2500553122](https://doi.org/10.1073/pnas.2500553122) (2025).
 
 ### Accessing ROADIES output files
 

docs/cite.md

@@ -2,7 +2,7 @@
 
 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).
+A. Gupta, S. Mirarab, & Y. Turakhia, Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES, Proc. Natl. Acad. Sci. U.S.A. 122 (19) e2500553122, [https://doi.org/10.1073/pnas.2500553122](https://doi.org/10.1073/pnas.2500553122) (2025).
 
 ## Accessing ROADIES output files
 

docs/install.md

@@ -116,4 +116,5 @@ source roadies_env.sh
 
 After successful setup (Setup complete message), your environment roadies_env will be activated. Proceed to Quick Start.
 
-**Note:** If you encounter issues with the Boost library, add its path to `$CPLUS_LIBRARY_PATH` and save it in `~/.bashrc`.
+!!! Note
+    If you encounter issues with the Boost library, add its path to `$CPLUS_LIBRARY_PATH` and save it in `~/.bashrc`.

docs/quickstart.md

@@ -2,17 +2,18 @@
 
 After installing using one of the options mentioned in Quick Install, you're ready to run ROADIES! To get started:
 
-1. Download the test dataset (11 Drosophila genomes):
+## Step 1: Download the test dataset (11 Drosophila genomes):**
 
 ```bash
 mkdir -p test/test_data && cat test/input_genome_links.txt | xargs -I {} sh -c 'wget -O test/test_data/$(basename {}) {}'
 ```
 
 This will save the datasets on a separate `test/test_data` folder within the repository
 
-2. Run the pipeline
+## Step 2: Run the pipeline
 
-#### IMPORTANT: ROADIES by default runs multiple iterations for generating highly accurate trees. For quick testing, use `--noconverge` to run a single iteration.
+!!! Note
+    ROADIES by default runs multiple iterations for generating highly accurate trees. For quick testing, use `--noconverge` to run a single iteration.
 
 ```bash
 python run_roadies.py --cores 16 # Full run (multiple iterations)
@@ -21,11 +22,12 @@ python run_roadies.py --cores 16 # Full run (multiple iterations)
 python run_roadies.py --cores 16 --noconverge # Quick test run (one iteration)
 ```
 
-3. Output:
+## Step 3: Analyze Output:
 
  - Final **UNROOTED** newick tree saved as `roadies.nwk` in a separate `output_files` folder. 
  - Intermediate files (if `--noconverge` not used) saved in a separate `converge_files` folder. 
 
 
-#### NOTE: ROADIES outputs unrooted trees by default. You can reroot trees on your own or use the provided `reroot.py` script in `workflow/scripts/` (given a reference rooted species tree as input). 
+!!! Note
+    ROADIES outputs unrooted trees by default. You can reroot trees on your own or use the provided `reroot.py` script in `workflow/scripts/` (given a reference rooted species tree as input).