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environment_osx.yml
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environment_osx.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: nf-core-kmermaid-0.1.0dev
channels:
- bioconda
- conda-forge
- defaults
- anaconda
dependencies:
- conda-forge::python=3.7.3
- conda-forge::markdown=3.1.1
- conda-forge::pymdown-extensions=6.0
- conda-forge::pygments=2.5.2
- conda-forge::tqdm=4.43.0
- conda-forge::clangxx_osx-64=11.1.0
- conda-forge::s3fs=0.4.2
- bioconda::sourmash=3.5.0
- bioconda::samtools=1.10
- bioconda::screed=1.0.4
- bioconda::khmer=3.0.0a3
- bioconda::pysam=0.16.0
- anaconda::make=4.2.1
- alabaster=0.7.12
- fastp=0.20.0
- fastqc=0.11.9
- matplotlib=3.1.1 # don't upgrade, multiqc conflict
- multiqc=1.8
- numpy=1.17.5
- pathos=0.2.5
- pip=20.0.2
- pytest=5.3.4
- seqtk=1.3
- ska=1.0
- sphinx=2.3.1
- jupyter=1.0.0
- sortmerna=2.1b # for metatranscriptomics
- ripgrep=12.1.1
- pip:
- bam2fasta==1.0.8
- orpheum==1.0.4