Python classes for interfacing with bed intervals
Project description
pybedlite
See documentation on pybedlite.readthedocs.org.
pip install pybedlite
OR
conda install -c bioconda pybedlite
OR
conda create -n pybedlite pybedlite
conda activate pybedlite
Requires python 3.8+ (for python < 3.8, please use pybedlite <= 0.0.3)
Getting Setup for Development Work
Clone the repository to your local machine. Note that pybedlite >= 0.0.4 includes cgranges as a submodule, so you must use the --recurse-submodules
option:
git clone --recurse-submodules https://github.com/fulcrumgenomics/pybedlite.git
Poetry is used to manage the python development environment.
A simple way to create an environment with the desired version of python and poetry is to use conda. E.g.:
conda create -n pybedlite python=3.8 poetry
conda activate pybedlite
poetry install
If the methods listed above do not work try the following:
mamba create -n pybedlite -c conda-forge "python=3.9.16" "poetry=1.6.1"
mamba activate pybedlite
poetry install
If, during poetry install
on Mac OS X errors are encountered running gcc/clang to build pybedtools
or other packages with native code, try setting the following and re-running poetry install
:
export CFLAGS="-stdlib=libc++"
Checking the Build
Run all checks with:
./ci/check.sh
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