Added Web UI for RNA seq pipeline

Web UI/.gitignore

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+/venv
+cre.txt
+exports.zip

Web UI/README.md

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+# Oxford Nanopore | RNA Analysis Tool
+### Welcome to the Oxford Nanopore RNA Analysis Tool repository!
+
+## Overview
+This repository contains the source code for our web application designed to simplify RNA sequence analysis using Oxford Nanopore sequencing data. Our goal is to provide a user-friendly interface that enables researchers, regardless of their programming background, to analyze RNA data efficiently and effectively.
+## Features
+
+- **User-Friendly Interface:** Our web application offers an intuitive interface designed for ease of use.
+- **Nanopore Sequencing Support:** Analyze RNA data generated from Oxford Nanopore sequencing technology.
+- **Simple Workflow:** Perform various analyses and visualizations with just a few clicks.
+- **Accessible to Non-Programmers:** No programming knowledge required. Anyone can analyze RNA data effortlessly.
+- **Interactive Visualizations:** Explore your RNA data through interactive charts and graphs.
+
+
+## Getting Started
+
+To get started with our RNA Analysis Tool, follow these steps:
+
+1. Clone this repository to your local machine.
+   ```
+   git clone https://github.com/KushanManahara/Oxford-Nanopore-RNA-Analysis-Tool.git
+   ```
+3. Navigate into the project repository.
+   ```
+   cd Oxford-Nanopore-RNA-Analysis-Tool
+   ```
+4. Create a virtual environment (not necessary)
+
+   In Windows
+   ```
+   python -m venv venv
+   ```
+
+   In Linux/MacOS
+   ```
+   python3 -m venv venv
+   ```
+6. Install the necessary dependencies as specified in the `requirements.txt` file.
+   ```
+   pip install -r requirements.txt
+   ```
+7. Run the web application using your preferred web server.
+   ```
+   streamlit run app.py
+   ```
+## Usage Instructions
+- Log in to your server using the provided `host` `username` and `password`.
+- Navigate to the **blasting page**.
+- Upload your `raw files` as a `.zip` file. The zip file should contain two files, one starting with `'pass_'` and the other with `'fail_'`.
+- The pipeline will run, generating the final blasting output as a zip file, which includes the **final blasting report**, **Venn diagram**, and **quality analysis report**.
+## Contributing
+
+We welcome contributions from the community! If you'd like to contribute to the development of the Oxford Nanopore RNA Analysis Tool, please fork this repository, make your changes, and submit a pull request.
+## Support
+
+If you encounter any issues or have any questions about using the Oxford Nanopore RNA Analysis Tool, please [open an issue](https://github.com/example/repository/issues) on this repository.## License
+
+
+This project is licensed under the [MIT License](LICENSE).
+
+## Tech Stack
+
+- Python
+- Streamlit
+
+
+## 🚀 About Me
+### Kushan Manahara
+
+I'm a final year undergraduate student pursuing Computer Engineering at the University of Peradeniya. My passion lies in research, AI development, and automation. I thrive on exploring new technologies and pushing the boundaries of what's possible in the realm of artificial intelligence.
+
+Whether it's diving into the intricacies of machine learning algorithms or crafting seamless user experiences through full stack development, I'm driven by a relentless curiosity and a desire to make meaningful contributions to the field of technology.
+
+Feel free to reach out if you'd like to collaborate on exciting projects or discuss ideas at the intersection of technology and innovation.
+
+Connect with me on [LinkedIn](Your_LinkedIn_Profile_URL) | Follow me on [Twitter](Your_Twitter_Profile_URL)
+
+## 🛠 Skills
+- **Full Stack Development**
+- **LLM Development** (Large Language Models)
+- **ML Development** (Machine Learning)
+## Authors
+
+- [@KushanManahara](https://github.com/KushanManahara/)
+## Badges
+[![MIT License](https://img.shields.io/badge/License-MIT-green.svg)](https://choosealicense.com/licenses/mit/)
+
+## 🔗 Links
+[![portfolio](https://img.shields.io/badge/my_portfolio-000?style=for-the-badge&logo=ko-fi&logoColor=white)](https://vercel.com/kushan-manaharas-projects/)
+[![linkedin](https://img.shields.io/badge/linkedin-0A66C2?style=for-the-badge&logo=linkedin&logoColor=white)](https://www.linkedin.com/in/kushan-manahara/)
+
+## Screenshots
+
+- ### Login Page ![App Screenshot](https://github.com/KushanManahara/Oxford-Nanopore-RNA-Analysis-Tool/assets/73605929/4f9939fa-db98-435b-a109-1a31945a5f02)
+
+- ### Blasting Page ![blasting page](https://github.com/KushanManahara/Oxford-Nanopore-RNA-Analysis-Tool/assets/73605929/7a41c018-5716-4b2f-9b76-31fd2ed239e2)

Web UI/app.py

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+import paramiko
+import streamlit as st
+import time
+
+
+def login():
+    def on_login():
+        try:
+            ssh_client = create_ssh_connection(host, username, password)
+
+            toast_placeholder = st.empty()
+            toast_placeholder.success("Login successful!")
+            ssh_client.close()
+            time.sleep(2)
+            toast_placeholder.empty()
+
+            title_placeholder.empty()
+            host_placeholder.empty()
+            username_placeholder.empty()
+            password_placeholder.empty()
+            st.session_state.logged_in = True
+            st.session_state.host = host
+            st.session_state.username = username
+            st.session_state.password = password
+            st.session_state.ssh_client = ssh_client
+
+        except Exception as e:
+            st.error(f"Login failed: {e}")
+
+    title_placeholder = st.empty()
+    host_placeholder = st.empty()
+    username_placeholder = st.empty()
+    password_placeholder = st.empty()
+    login_button_placeholder = st.empty()
+
+    title_placeholder.title("Login Page")
+
+    host = host_placeholder.text_input("Host")
+    username = username_placeholder.text_input("Username")
+    password = password_placeholder.text_input("Password", type="password")
+
+    if host and username and password:
+        print(host)
+        print(username)
+        print(password)
+        if not login_button_placeholder.button("Login", on_click=on_login):
+            st.error("Invalid hostname, username or password, . Please try again.")
+
+
+def create_ssh_connection(host, username, password):
+    ssh_client = paramiko.SSHClient()
+    ssh_client.set_missing_host_key_policy(paramiko.AutoAddPolicy())
+    ssh_client.connect(hostname=host, username=username, password=password)
+    return ssh_client
+
+
+def create_project_dir(ssh_client, folder_name):
+    ssh_client.exec_command(f"mkdir -p WebApp/{folder_name}")
+    ssh_client.exec_command(f"mkdir -p WebApp/{folder_name}/test-dir")
+    ssh_client.exec_command(f"mkdir -p WebApp/{folder_name}/EXPORTS")
+    ssh_client.exec_command(
+        f'echo "Hello World" > WebApp/{folder_name}/hello-world.txt'
+    )
+
+
+def download_file(ssh_client, remote_path, local_path):
+    sftp_client = ssh_client.open_sftp()
+    sftp_client.get(remote_path, local_path)
+    sftp_client.close()
+
+
+def create_zip_folder(ssh_client, folder_path, zip_file_path):
+    # Execute the zip command remotely to create the zip file
+    ssh_client.exec_command(f"zip -r {zip_file_path} {folder_path}")
+
+
+def project_init():
+    st.title("Project Init Page")
+    st.write("Welcome to the Project Init Page! You can start project init here.")
+
+
+def blasting(host, username, password):
+    if not st.button("Back", on_click=logout):
+        st.title("Blasting Page")
+        folder_name = st.text_input("Project Name")
+        uploaded_file = st.file_uploader("Upload FAST5 file as a zip", type=["zip"])
+
+        project_status = st.empty()
+
+        if st.button("Start Blasting"):
+            try:
+                project_status.info("Project initializing started...")
+                ssh_client = create_ssh_connection(host, username, password)
+                create_project_dir(ssh_client, folder_name)
+                project_status.success(
+                    f"Project '{folder_name}' is initiated successfully!"
+                )
+                time.sleep(1)
+                project_status.empty()
+
+                ssh_client.close()
+            except Exception as e:
+                project_status.error(f"An error occurred: {e}")
+                time.sleep(3)
+                project_status.empty()
+
+            if uploaded_file is not None:
+                project_status.empty()
+                try:
+                    project_status.info("Uploading project files...")
+                    ssh_client = create_ssh_connection(host, username, password)
+                    with ssh_client.open_sftp() as sftp:
+                        with sftp.file(
+                            f"WebApp/{folder_name}/{uploaded_file.name}", "wb"
+                        ) as f:
+                            f.write(uploaded_file.getvalue())
+                    project_status.success("Project file are uploaded successfully!")
+
+                    # blasting is started
+                    time.sleep(1)
+                    project_status.info("Blasting started...")
+                    time.sleep(2)
+                    project_status.success("Blasting Completed...")
+                    time.sleep(2)
+                    project_status.empty()
+
+                    # TODO:
+
+                    # create a zip file of whole final project
+                    create_zip_folder(
+                        ssh_client,
+                        f"WebApp/{folder_name}",
+                        f"WebApp/{folder_name}/EXPORTS/exports.zip",
+                    )
+
+                    project_status.info("Completed project files are Downloading...")
+
+                    # Download the project export file from the remote server
+                    download_file(
+                        ssh_client,
+                        f"WebApp/{folder_name}/EXPORTS/exports.zip",
+                        "exports.zip",
+                    )
+
+                    project_status.success(
+                        "Completed project files are Downloaded successfully!"
+                    )
+
+                except Exception as e:
+                    project_status.error(f"An error occurred while uploading file: {e}")
+                    ssh_client.close()
+
+
+# Main function
+def logout():
+    st.session_state.logged_in = False
+
+
+def main():
+    global ssh_client, host, username, password
+
+    if "logged_in" not in st.session_state:
+        host = "localhost"
+        st.session_state.logged_in = False
+
+    if not st.session_state.logged_in:
+        login()
+
+    else:
+        blasting(
+            st.session_state.host, st.session_state.username, st.session_state.password
+        )
+
+
+# Run the main function
+if __name__ == "__main__":
+    main()

Web UI/requirements.txt

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+paramiko==3.4.0
+streamlit==1.32.2
+pyscp==1.1.20