alabtools

Package for working with the data in Frank Alber's lab at the University of California Los Angeles for 3D genome analysis and modeling. See also our Integrative Genome Modeling (IGM) software package: https://github.com/alberlab/igm.git.

Installation

ATTENTION: This package should work on both Linux and MacOS systems. It has been tested on CentOS 7.9.2009 (Core) and on Mac Tahoe 26.2.

Make sure you have conda installed (https://docs.conda.io/en/latest/miniconda.html) and that you have added the conda-forge channel (https://conda-forge.org/).

Create a conda environment with a Python 3.11 version.

conda create -n alab python=3.11 -y
conda activate alab

Then, install the following packages with conda forge:

conda install -c conda-forge \
    numpy \
    scipy \
    pandas \
    h5py \
    hdf5 \
    matplotlib \
    cython \
    swig \
    ipyparallel \
    cloudpickle \
    tqdm \
    six \
    -y

Then install another set of packages with pip:

pip install cooler pyBigWig

Finally, install the alabtools package:

pip install git+https://github.com/alberlab/alabtools.git

If the install fails with build-isolation / NumPy build errors (common on older HPC systems):

pip install git+https://github.com/alberlab/alabtools.git --no-build-isolation