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environment.yml
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environment.yml
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# You can use this file to create a conda environment for this pipeline:
# conda env create -f environment.yml
name: systemsgenetics-gemmaker-2.1.1
channels:
- conda-forge
- bioconda
- defaults
dependencies:
# nf-core dependencies
- conda-forge::python=3.9.2
- conda-forge::markdown=3.3.4
- conda-forge::pymdown-extensions=8.1.1
- conda-forge::pygments=2.8.1
# Software dependencies here
- conda-forge::pandas=1.2.3
- conda-forge::numpy=1.20.2
- conda-forge::xmltodict=0.12.0
- conda-forge::tbb=2020.2
- conda-forge::requests=2.23.0
- conda-forge::jinja2=2.10
- conda-forge::biopython=1.79
# Use version 2.10.0 to avoid a vdb-config problem with singularity
- bioconda::sra-tools=2.10.0
- bioconda::trimmomatic=0.39
- bioconda::gffread=0.12.1