From 22066456845f25d033075445086d4c68ba26a072 Mon Sep 17 00:00:00 2001 From: ang037 Date: Tue, 27 May 2025 07:21:01 -0700 Subject: [PATCH] updated PASTA source code instructions --- README.md | 78 +++++++++++++++++++++++++++++----------------- docs/install.md | 22 ++++++++++++- docs/quickstart.md | 2 ++ 3 files changed, 72 insertions(+), 30 deletions(-) diff --git a/README.md b/README.md index 936e4113..84271e6b 100644 --- a/README.md +++ b/README.md @@ -63,7 +63,7 @@ Please follow any of the options below to install ROADIES in your system. **Step 1:** Install Conda (if not installed): -``` +```bash wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh chmod +x Miniconda3-latest-Linux-x86_64.sh ./Miniconda3-latest-Linux-x86_64.sh @@ -74,13 +74,13 @@ source ~/.bashrc **Step 2:** Configure Conda channels: -``` +```bash conda config --add channels defaults ``` -``` +```bash conda config --add channels bioconda ``` -``` +```bash conda config --add channels conda-forge ``` @@ -88,25 +88,45 @@ Verify the installation by running `conda` in your terminal **Step 3:** Create and activate a custom environment: -``` +```bash conda create -n roadies_env python=3.9 ete3 seaborn ``` -``` +```bash conda activate roadies_env ``` **Step 4:** Install ROADIES: -``` +```bash conda install roadies=0.1.10 ``` **Step 5:** Locate the installed files: -``` +```bash cd $CONDA_PREFIX/ROADIES ``` -You will be able to find the contents of the repository within this ROADIES folder. Now you are ready to follow the [Quick Start](#start) section to run the pipeline. +Now, you will be able to find the contents of the repository within this ROADIES folder. + +**Step 6:** Run the following commands: + +```bash +git clone https://github.com/smirarab/pasta.git +git clone https://github.com/smirarab/sate-tools-linux.git +cd pasta +python3 setup.py develop --user +``` + +Also, in the `align.smk` file (inside the `workflow/rules` directory of the ROADIES repository), please replace any instance of: + +- `pasta.py` with `python pasta/run_pasta.py` +- `run_seqtools.py` with `python pasta/run_seqtools.py` + +After following all these steps, now you are ready to follow the [Quick Start](#start) section to run the pipeline. Make sure to go back to the main directory to follow the next steps: + +```bash +cd ROADIES +``` ### Option 2: Install via DockerHub @@ -114,12 +134,12 @@ If you would like to install ROADIES using DockerHub, follow these steps: **Step 1:** Pull the ROADIES image from DockerHub: -``` +```bash docker pull ang037/roadies:latest ``` **Step 2:** Launch a container: -``` +```bash docker run -it ang037/roadies:latest ``` @@ -129,19 +149,19 @@ These commands will launch the Docker container in interactive mode, with the `r **Step 1:** Clone the ROADIES repository: -``` +```bash git clone https://github.com/TurakhiaLab/ROADIES.git ``` -``` +```bash cd ROADIES ``` **Step 2:** Build and run the Docker container: -``` +```bash docker build -t roadies_image . ``` -``` +```bash docker run -it roadies_image ``` @@ -161,25 +181,25 @@ Once you are able to access the ROADIES repository, refer to [Quick Start](#star For Ubuntu, you can install these dependencies with: -``` +```bash sudo apt-get install -y wget unzip make g++ python3 python3-pip python3-setuptools git default-jre libgomp1 libboost-all-dev cmake ``` **Step 2:** Clone the repository: -``` +```bash git clone https://github.com/TurakhiaLab/ROADIES.git ``` -``` +```bash cd ROADIES ``` **Step 3:** Run the installation script: -``` +```bash chmod +x roadies_env.sh ``` -``` +```bash source roadies_env.sh ``` @@ -193,9 +213,9 @@ After successful setup (Setup complete message), your environment `roadies_env` After installing using one of the options mentioned in [Quick Install](#usage), you're ready to run ROADIES! To get started: -**Step 1:** Download the test dataset (11 Drosophila genomes): +**Step 1:** Download the test dataset (11 Drosophila genomes) (make sure to perform this step from the main repository directory): -``` +```bash mkdir -p test/test_data && cat test/input_genome_links.txt | xargs -I {} sh -c 'wget -O test/test_data/$(basename {}) {}' ``` @@ -206,13 +226,13 @@ This will save the datasets on a separate `test/test_data` folder within the rep #### IMPORTANT: ROADIES by default runs multiple iterations for generating highly accurate trees. For quick testing, use `--noconverge` to run a single iteration. **Full run (multiple iterations) - Default** -``` +```bash python run_roadies.py --cores 16 ``` **OR** **Quick test run (one iteration)** -``` +```bash python run_roadies.py --cores 16 --noconverge ``` @@ -239,7 +259,7 @@ If you want to run ROADIES with your own datasets, follow these steps: **IMPORTANT**: Each file must contain only one species. If needed, split multi-species files with: -``` +```bash faSplit byname ``` @@ -250,20 +270,20 @@ faSplit byname **Step 3:** Run the Pipeline: -``` +```bash python run_roadies.py --cores 16 ``` **Modes of operation**: ROADIES supports multiple modes of operation (`fast`, `balanced`, `accurate`) by controlling the accuracy-runtime tradeoff. Use any one of the following commands to select a mode (`accurate` mode is the default): -``` +```bash python run_roadies.py --cores 16 --mode accurate ``` -``` +```bash python run_roadies.py --cores 16 --mode balanced ``` -``` +```bash python run_roadies.py --cores 16 --mode fast ``` diff --git a/docs/install.md b/docs/install.md index 69558a77..5abd281a 100644 --- a/docs/install.md +++ b/docs/install.md @@ -50,7 +50,27 @@ conda install roadies=0.1.10 cd $CONDA_PREFIX/ROADIES ``` -You will be able to find the contents of the repository within this ROADIES folder. Now you are ready to follow the Quick Start section to run the pipeline. +Now, you will be able to find the contents of the repository within this ROADIES folder. + +6. Run the following commands: + +```bash +git clone https://github.com/smirarab/pasta.git +git clone https://github.com/smirarab/sate-tools-linux.git +cd pasta +python3 setup.py develop --user +``` + +Also, in the `align.smk` file (inside the `workflow/rules` directory of the ROADIES repository), please replace any instance of: + +- `pasta.py` with `python pasta/run_pasta.py` +- `run_seqtools.py` with `python pasta/run_seqtools.py` + +After following all these steps, now you are ready to follow the Quick Start section to run the pipeline. Make sure to go back to the main directory to follow the next steps: + +```bash +cd ROADIES +``` ## Option 2: Install via DockerHub diff --git a/docs/quickstart.md b/docs/quickstart.md index e4288fbd..5a2f72f2 100644 --- a/docs/quickstart.md +++ b/docs/quickstart.md @@ -4,6 +4,8 @@ After installing using one of the options mentioned in Quick Install, you're rea ## Step 1: Download the test dataset (11 Drosophila genomes):** +Make sure to run this step from the main ROADIES repository directory. + ```bash mkdir -p test/test_data && cat test/input_genome_links.txt | xargs -I {} sh -c 'wget -O test/test_data/$(basename {}) {}' ```