Installation

Required Packages

The following software must be installed on your machine:

Python (required 3.7+, tested with version 3.9)

Python dependencies

matplotlib (tested 3.9.2)
numpy (tested 1.26.4)
pandas (tested 2.2.3)
PyQt5 (tested 5.15.11)
scikit-learn (tested 1.5.2)
cooler (tested 0.10.2)
sortedcontainers (tested 2.4.0)
pomegranate (tested 0.15.0)
scikit-image (tested 0.24.0)
wget (tested 3.2)

Installation

DeCGR and all dependencies can be installed using pip:

$ conda config --add channels r
$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
$ conda create -n DeCGR python=3.9 rpy2 r-mgcv
$ conda activate DeCGR
$ pip install -U DeCGR

Notes for Installation on Windows Systems

Avoid PowerShell: Use Command Prompt instead of PowerShell for the installation, as certain commands may not work correctly in PowerShell.
Installation Error: Encountering the error “error: Microsoft Visual C++ 14.0 or greater is required.”

Solution: Refer to this guide.

Running

Use the command below to access the DeCGR interface.

Mac OS or Linux (Recommended)

$ DeCGR

Windows

$ DeCGR_windows

Notes for Running on Windows Systems

On Windows systems, packages like rpy2 may not be fully compatible, which can lead to various issues during runtime. Below are common problems and their solutions for user reference:

JIT Initialization Error: Encountering “fatal error unable to initialize the jit” when executing DeCGR_windows.

Solution:
```
$ set R_HOME=%CONDA_PREFIX%\Lib\R
```
Missing ‘stats’ Package: Error “package ‘stats’ in options(‘defaultPackages’) was not found” when running the Fragment Assembly or visualization modules.

Solution:
```
$ set ENV_PATH=%CONDA_PREFIX%

$ xcopy "%ENV_PATH%\Lib\R\bin\x64\*.*" "%ENV_PATH%\Lib\R\library\stats\libs\x64" /S /I
```

Test Data

Tumor Hi-C data: K562 cell line (4DNFI18UHVRO.mcool) can be downloaded from 4dnucleome.

Control Hi-C data: GM12878 cell line (4DNFITRVKRPA.mcool) can be downloaded from 4dnucleome.

Breakpoint file (for Module2): This file is named “K562_chr18_breakpoint.txt” and provided in the DeCGR.

Assembly result file (for Module3): This file is named “K562_chr18_assembly_result.txt” and provided in the DeCGR.

Complex rearrangement file (for Module4): This file is named “K562_chr18_CGR.txt” and provided in the DeCGR.