Merge pull request #48 from TurakhiaLab/package_updates

changes to README for better readability

Author: ang037

README.md

@@ -75,7 +75,11 @@ source ~/.bashrc
 
 ```
 conda config --add channels defaults
+```
+```
 conda config --add channels bioconda
+```
+```
 conda config --add channels conda-forge
 ```
 
@@ -85,23 +89,23 @@ Verify the installation by running `conda` in your terminal
 
 ```
 conda create -n roadies_env python=3.9 ete3 seaborn
+```
+```
 conda activate roadies_env
 ```
 
 4. Install ROADIES:
 
 ```
-conda install roadies
+conda install roadies=0.1.10
 ```
 
 5. Locate the installed files:
 
 ``` 
-cd $CONDA_PREFIX/envs/roadies_env/ROADIES
-
+cd $CONDA_PREFIX/ROADIES
 ```
-
-Now you are ready to follow the [Quick Start](#start) section to run the pipeline. 
+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. 
 
 ### <a name="dockerhub"></a> Option 2: Install via DockerHub
 
@@ -118,21 +122,25 @@ docker pull ang037/roadies:latest
 docker run -it ang037/roadies:latest
 ```
 
-Once you are able to access the ROADIES repository, refer to the [Quick Start](#start) to run the pipeline. 
+These commands will launch the Docker container in interactive mode, with the roadies_env environment activated and the working directory set to the ROADIES repository containing all necessary files. Once you are able to access the ROADIES repository, refer to the [Quick Start](#start) to run the pipeline. 
 
 ### <a name="docker"></a> Option 3: Install via Local Docker Build
 
 1. Clone the ROADIES repository:
 
 ```
 git clone https://github.com/TurakhiaLab/ROADIES.git
+```
+```
 cd ROADIES
 ```
 
 2. Build and run the Docker container:
 
 ```
 docker build -t roadies_image .
+```
+```
 docker run -it roadies_image
 ```
 
@@ -160,17 +168,21 @@ sudo apt-get install -y wget unzip make g++ python3 python3-pip python3-setuptoo
 
 ```
 git clone https://github.com/TurakhiaLab/ROADIES.git
+```
+```
 cd ROADIES
 ```
 
 3. Run the installation script:
 
 ```
 chmod +x roadies_env.sh
+```
+```
 source roadies_env.sh
 ```
 
-After successful setup (Setup complete message), your environment roadies_env will be activated. Proceed to [Quick Start](#start).
+After successful setup (Setup complete message), your environment `roadies_env` will be activated. Proceed to [Quick Start](#start).
 
 **Note:** If you encounter issues with the Boost library, add its path to `$CPLUS_LIBRARY_PATH` and save it in `~/.bashrc`.
 
@@ -192,11 +204,15 @@ 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)**
 ```
-python run_roadies.py --cores 16 # Full run (multiple iterations)
+python run_roadies.py --cores 16 
 ```
+**OR**
+
+**Quick test run (one iteration)**
 ```
-python run_roadies.py --cores 16 --noconverge # Quick test run (one iteration)
+python run_roadies.py --cores 16 --noconverge 
 ```
 
 3. Output:
@@ -240,9 +256,11 @@ python run_roadies.py --cores 16
 
 ```
 python run_roadies.py --cores 16 --mode accurate
-
+```
+```
 python run_roadies.py --cores 16 --mode balanced
-
+```
+```
 python run_roadies.py --cores 16 --mode fast
 ```
 

docs/install.md

@@ -19,7 +19,11 @@ source ~/.bashrc
 
 ```bash
 conda config --add channels defaults
+```
+```bash
 conda config --add channels bioconda
+```
+```bash
 conda config --add channels conda-forge
 ```
 
@@ -29,23 +33,24 @@ Verify the installation by running `conda` in your terminal
 
 ```bash
 conda create -n roadies_env python=3.9 ete3 seaborn
+```
+```bash
 conda activate roadies_env
 ```
 
 4. Install ROADIES:
 
 ```bash
-conda install roadies
+conda install roadies=0.1.10
 ```
 
 5. Locate the installed files:
 
 ```bash
-cd $HOME/miniconda3/envs/roadies_env/ROADIES
-
+cd $CONDA_PREFIX/ROADIES
 ```
 
-Now you are ready to follow the Quick Start section to run the pipeline. 
+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. 
 
 ## Option 2: Install via DockerHub
 
@@ -62,21 +67,25 @@ docker pull ang037/roadies:latest
 docker run -it ang037/roadies:latest
 ```
 
-Once you are able to access the ROADIES repository, refer to the Quick Start section to run the pipeline. 
+These commands will launch the Docker container in interactive mode, with the roadies_env environment activated and the working directory set to the ROADIES repository containing all necessary files. Once you are able to access the ROADIES repository, refer to the Quick Start section to run the pipeline. 
 
 ## Option 3: Install via Local Docker Build
 
 1. Clone the ROADIES repository:
 
 ```bash
 git clone https://github.com/TurakhiaLab/ROADIES.git
+```
+```bash
 cd ROADIES
 ```
 
 2. Build and run the Docker container:
 
 ```bash
 docker build -t roadies_image .
+```
+```bash
 docker run -it roadies_image
 ```
 
@@ -104,17 +113,21 @@ sudo apt-get install -y wget unzip make g++ python3 python3-pip python3-setuptoo
 
 ```bash
 git clone https://github.com/TurakhiaLab/ROADIES.git
+```
+```bash
 cd ROADIES
 ```
 
 3. Run the installation script:
 
 ```bash
 chmod +x roadies_env.sh
+```
+```bash
 source roadies_env.sh
 ```
 
-After successful setup (Setup complete message), your environment roadies_env will be activated. Proceed to Quick Start.
+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`.

docs/quickstart.md

@@ -15,11 +15,15 @@ This will save the datasets on a separate `test/test_data` folder within the rep
 !!! Note
     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)**
 ```bash
-python run_roadies.py --cores 16 # Full run (multiple iterations)
+python run_roadies.py --cores 16
 ```
+**OR**
+
+**Quick test run (one iteration)**
 ```bash
-python run_roadies.py --cores 16 --noconverge # Quick test run (one iteration)
+python run_roadies.py --cores 16 --noconverge 
 ```
 
 ## Step 3: Analyze Output:

docs/usage.md

@@ -120,7 +120,7 @@ For extensive debugging, other intermediate output files for each stage of the p
 7. `ref_dist.csv` - this file provides the iteration number, number of gene trees and the Normalized Robinson-Foulds distance between the final estimated species tree (i.e., `roadies.nwk`) and the reference tree (i.e., REFERENCE parameter in `config.yaml`), for all iterations.
 8. `time_stamps.csv`- this file contains the start time in first line, iteration number, number of gene trees required for estimating species tree, end time, and total runtime (in seconds), respectively, for all iterations in subsequent lines.
 
-# Run ROADIES in a multi-node cluster (using SLURM)
+# Run ROADIES in a multi-node cluster (using SLURM) (currently being tested)
 
 To run ROADIES in a multi-node cluster, make the following changes in the file `workflow/scripts/converge.py` (for `--noconverge` mode - make changes in `workflow/scripts/noconverge.py`)