updated PASTA source code instructions

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
@@ -74,52 +74,72 @@ 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
 ```
 
 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
+```
 
 ### <a name="dockerhub"></a> Option 2: Install via DockerHub
 
 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 <input_dir> <output_dir>
 ```
 
@@ -250,20 +270,20 @@ faSplit byname <input_dir> <output_dir>
 
 **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
 ```
 

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
 

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 {}) {}'
 ```