run-dipc 1.9.4

Diploid chromatin conformation capture analysis

Dip-C

Diploid Chromatin Conformation Capture — reconstruct 3D diploid genomes from single cells.

Installation

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 typically happens on CentOS/RHEL 7 (end-of-life June 2024), which ships GCC 4.8.

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

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):

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

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

License

MIT