Installation

Cis-GS ships in three flavours. Pick whichever matches your situation.

From PyPI (recommended)

pip install cis-gs

That installs both entry points:

cis-gs --help          # interactive CLI
cis-gs-gui             # PyQt5 GUI

Requires Python 3.9 or newer.

Standalone Windows executable 

Grab Cis-GS.exe from the latest GitHub release. Double-click — no Python install required. ~120 MB single file.

From source (for development)

git clone https://github.com/Ayushmania2002/Cis-GS.git
cd Cis-GS
python -m venv venv
source venv/bin/activate              # Windows: venv\Scripts\activate
pip install -e ".[dev,docs]"
python app_v4_open.py                 # launch GUI
python -m cis_gs --help               # CLI

Building the .exe yourself 

setup_and_build.bat

See the BUILD.md in the repo root for the PyInstaller spec, macOS/Linux build scripts, and the PyPI release workflow.

First-run setup 

On first launch the GUI asks for your NCBI email (required by Entrez for any genome download). It is stored only in ~/CisGS-Workspace/.ncbi_email and is never transmitted anywhere except to NCBI on your own requests.

Workspace location 

All Cis-GS outputs land in ~/CisGS-Workspace/ by default. Change it from Settings → Change Workspace in the GUI.