Metadata-Version: 2.4
Name: run-dipc
Version: 1.9.6
Summary: Diploid chromatin conformation capture analysis
Author: Longzhi Tan
License: MIT License
        
        Copyright (c) 2018 Longzhi Tan and contributors
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: Homepage, https://github.com/tanlongzhi/dip-c
Project-URL: Repository, https://github.com/tanlongzhi/dip-c
Keywords: bioinformatics,chromatin,Hi-C,3D genome,single-cell
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=1.22
Requires-Dist: scipy>=1.7
Requires-Dist: rmsd>=1.5
Requires-Dist: mmcif-pdbx>=2.0
Requires-Dist: pysam>=0.20
Provides-Extra: dev
Requires-Dist: pytest>=7.0; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Dynamic: license-file

# Dip-C

**Dip**loid **C**hromatin Conformation Capture — reconstruct 3D diploid genomes from single cells.

## Installation

```bash
pip install run-dipc
```

### Troubleshooting: old Linux systems (CentOS/RHEL 7)

If `pip install` fails with **`NumPy requires GCC >= 9.3`**, your system's
default compiler is too old to build NumPy from source. This can happen on
older Linux distributions that ship with GCC 4.8.

**Option A** — load a newer compiler (HPC clusters usually have one):

```bash
module avail gcc          # see what's available
module load gcc/11.2.0    # load any version >= 9.3
pip install run-dipc
```

**Option B** — install NumPy and SciPy from conda first (provides prebuilt
binaries, no compiler needed):

```bash
conda install numpy scipy
pip install run-dipc
```

You can check your GCC version with `gcc --version` and your OS with
`cat /etc/os-release`. Please contact your system administrator if
this is a problem for you.

## Usage

```bash
dip-c <command> [options]
```

Run `dip-c` with no arguments to see all available commands.

## Documentation

Full documentation, workflows, and file format specifications are available on GitHub:

**https://github.com/tanlongzhi/dip-c**

## Citations

Please cite the original Dip-C paper:

> Tan, Longzhi\*; Xing, Dong\*; Chang, Chi-Han; Li, Heng; Xie, X. Sunney "Three-dimensional genome structures of single diploid human cells," *Science* **361**, 924-928 (2018). [DOI:10.1126/science.aat5641](https://doi.org/10.1126/science.aat5641)

## License

MIT
