From 8616755f2a0193490d0ca470447163714dc63571 Mon Sep 17 00:00:00 2001 From: ang037 Date: Sun, 27 Apr 2025 00:14:37 -0700 Subject: [PATCH 1/2] cleaned further --- docs/install.md | 3 ++- docs/quickstart.md | 12 +++++++----- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/docs/install.md b/docs/install.md index 11aa8f3a..70a71752 100644 --- a/docs/install.md +++ b/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 `$CPLUS_LIBRARY_PATH` and save it in `~/.bashrc`. \ No newline at end of file +!!! Note + If you encounter issues with the Boost library, add its path to `$CPLUS_LIBRARY_PATH` and save it in `~/.bashrc`. diff --git a/docs/quickstart.md b/docs/quickstart.md index 7a14a631..c845cce7 100644 --- a/docs/quickstart.md +++ b/docs/quickstart.md @@ -2,7 +2,7 @@ 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 {}) {}' @@ -10,9 +10,10 @@ mkdir -p test/test_data && cat test/input_genome_links.txt | xargs -I {} sh -c ' 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). From c17f6b4d5cd0eb71d562b907c82b163dbab8df7e Mon Sep 17 00:00:00 2001 From: ang037 Date: Sat, 10 May 2025 01:23:43 -0700 Subject: [PATCH 2/2] updated citations --- README.md | 6 +++--- docs/cite.md | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index d7d9d094..0a750301 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ [](https://snakemake.readthedocs.io/en/v7.19.1/index.html) [](http://bioconda.github.io/recipes/roadies/README.html) [](https://hub.docker.com/r/ang037/roadies) -[](https://www.biorxiv.org/content/10.1101/2024.05.27.596098v1) +[](https://doi.org/10.1073/pnas.2500553122) [](https://doi.org/10.5061/dryad.tht76hf73) [](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 diff --git a/docs/cite.md b/docs/cite.md index d93756c5..cce2d6b1 100644 --- a/docs/cite.md +++ b/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