ogtk 0.1.5

General tools for genomics and lineage tracing

Olivares Genomic toolkit

Installation

Basic Installation

Linux/Windows

pip install ogtk

macOS

macOS requires additional system dependencies before installation:

1. Install LLVM and OpenMP support:

brew install llvm

2. 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"

3. Reload your shell configuration:

source ~/.zshrc  # or source ~/.bash_profile

4. 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

1. Install system dependencies:

brew install llvm patchelf

2. Set up the environment as described above

3. 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:

1. Make sure LLVM is properly installed: brew install llvm
2. Verify environment variables are set correctly
3. 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.

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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.