StreamChol

This is a web application for predicting drug-like compounds that may induce cholestasis. The methodology is based on the article we published: https://pubs.acs.org/doi/10.1021/acs.jcim.3c00945.

StreamChol in Docker hub

A docker container (https://www.docker.com/), fully configured can be downloaded from DockerHub and installed using:

docker run -d -p 8501:8501 parodbe/streamchol_app

Then, the StreamChol will be accesible from a web browser at address http://localhost:8501

Stand-alone Deployment

These steps will guide you through running the app directly on your local machine without Docker.

Prerequisites

Ensure your system meets the following requirements:

• R: Version 4.0 or higher
• Rtools (Windows only)
• Microsoft Build Tools (Windows only)
• Python: Version 3.8 or higher (if applicable)
• Properly configured environment variables (details below)

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Installation Steps

Step 1: Install R

1. Download the latest version of R from CRAN.
2. Install R:
   • macOS: Drag the R package to the Applications folder.
   • Windows: Run the .exe installer and follow the on-screen instructions.
   • Linux: Use your package manager:

     sudo apt update
     sudo apt install r-base

3. Verify the installation:

   R --version

Step 2: Install Rtools (Windows Only)

1. Download Rtools from Rtools for Windows.
2. Install Rtools and ensure that its path is added to your system environment variables.
3. Verify the installation:

   R CMD config --ldflags

Step 3: Install Microsoft Build Tools (Windows Only)

1. Download and install Microsoft Build Tools from Visual Studio Build Tools.
2. During installation, select the following:
   • Workload: "Desktop Development with C++".
   • Individual Components:
     • MSVC Compiler
     • Windows 10/11 SDK
     • CMake tools (optional but recommended)
3. Verify the installation:

   cl

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2. Configuring Environment Variables

For R

1. Add the R installation directory to your PATH:
   • Example:

     C:\Program Files\R\R-4.4.2\bin\x64
     

2. Verify:

   R --version

For Rtools

1. Add the Rtools directory to your PATH:
   • Example for Rtools44:

     C:\rtools44\usr\bin
     C:\rtools44\x86_64-w64-mingw32.static.posix\bin
     

2. Verify:

   gcc --version

For Microsoft Build Tools

1. Add the directory containing cl.exe to your PATH:
   • Example:

     C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\<version>\bin\Hostx64\x64
     

2. Verify:

   cl

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3. Install Required Libraries

For R

Run the following in an R console:

install.packages(c("httk", "dplyr", "stringr"))
# Add any other packages your app requires

For Python

If your app uses Python, install the required libraries:

1. Install Python:

   python --version

   Make sure Python is in your PATH.

2. Install dependencies:

   pip install -r requirements.txt

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4. Run the application

1. To activate in the app.py file the following steps to set the R environment:

   os.environ["R_HOME"] = 'C:/Program Files/R/R-4.4.12' 
   os.environ["PATH"] = 'C:/Program Files/R/R-4.4.2/bin/x64' + ";" + os.environ["PATH"]

2. Run streamlit app.py

   http://localhost:8501