Olivares Genomic toolkit
Installation
Basic Installation
Linux/Windows
pip install ogtk
macOS
macOS requires additional system dependencies before installation:
- Install LLVM and OpenMP support:
brew install llvm
- Set up the environment (add this to your ~/.zshrc or ~/.bash_profile):
export PATH="/opt/homebrew/opt/llvm/bin:$PATH"
export CC=/opt/homebrew/opt/llvm/bin/clang
export CXX=/opt/homebrew/opt/llvm/bin/clang++
export LDFLAGS="-L/opt/homebrew/opt/llvm/lib"
export CPPFLAGS="-I/opt/homebrew/opt/llvm/include"
- Reload your shell configuration:
source ~/.zshrc # or source ~/.bash_profile
- Install the package:
pip install ogtk
#or for all-inclusive functionality
pip install 'ogtk[sc,rs']
With Rust Support
Linux
pip install ogtk[rs]
macOS
- Install system dependencies:
brew install llvm patchelf
-
Set up the environment as described above
-
Install the package:
pip install ogtk[rs]
astral uv
After having installed astral-uv
curl -LsSf https://astral.sh/uv/install.sh | sh
Initialize project and add packages.
uv init uvogtk
cd uvogtk
add ogtk
add ipython
uv venv --python 3.10
uv sync
Troubleshooting
If you encounter build errors related to OpenMP on macOS:
- Make sure LLVM is properly installed:
brew install llvm - Verify environment variables are set correctly
- Try reinstalling with:
pip install --no-cache-dir ogtk
For other platforms, if you see OpenMP-related errors:
- Ubuntu/Debian:
sudo apt-get install libomp-dev - Fedora:
sudo dnf install libomp-devel
Functionality
Three main modules are supported.
ltr
Comprehends lineage tracing analysis for bulk and single-cell data a various modalities. It is capable of pre-processing of multi-site lineage reporters such as GESTALT in addition to single-sites, namely shRNA.
UM
This represents the main workframe for treating with single-molecule data.
Utils
Various recipes for anlayising single-cell RNA-seq data (metacells and single-cells) and implements wrappers for other genomic toolkits such as bbtools.
Migration to pola-rs is work in progress but largely supported.
Notes:
If there are problems with missing zlib-devel not found install pysam via conda/mamba since zlib-devel cannot be installed using pip.
1 maintainer
Metadata
1 maintainer
Release files for ogtk 0.1.8
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| ogtk-0.1.8.tar.gz | 1.8 MB | With provenance | Details for ogtk-0.1.8.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| ogtk-0.1.8-py2.py3-none-any.whl | Python 2, Python 3 | none | any | Details for ogtk-0.1.8-py2.py3-none-any.whl |
Total release size: 2.0 MB
Release files / ogtk-0.1.8.tar.gz
| Download URL | ogtk-0.1.8.tar.gz |
|---|---|
| Size | 1.8 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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| Download URL | ogtk-0.1.8-py2.py3-none-any.whl |
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| Size | 211.8 kB |
| Tags | Python 2 Python 3 |
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SHA-256 checksum How to use checksums |
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Yes |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Provenance
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PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on May 13, 2025.
Transparency logSecurity for ogtk 0.1.8
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Attestation for ogtk-0.1.8.tar.gz
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PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on May 13, 2025.
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