dp_tools_setup

Code below is for this link: https://github.com/AstrobioMike/dp_tools/tree/mike-dev

You will need to change the git clone command below accordingly to be your username and your branch name.

Cloning and installing

# cloning just wanted branch
git clone -b mike-dev https://github.com/AstrobioMike/dp_tools.git

# making virtual env (six, requests, and rich i needed when doing local nextflow runs (even though they worked when outside nextflow) so just added here)
mamba create -y -n dp-tools-dev -c conda-forge -c bioconda -c defaults python=3 samtools=1.15.1 pytest=7.1.3 six requests rich
conda activate dp-tools-dev

# installing in "development mode" (so we can edit code that the package recognizes and uses)
pip install --editable dp_tools/

# quick test that it can find modules
dpt-get-isa-archive -h

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Note for Mike (this is done above also now)

When testing local nextflow workflows with the above install, libraries were missing (even though they worked outside of nextflow/pip shows them installed already). Adding them with conda worked though:

mamba install -c conda-forge six requests rich