micos-2024/environment.yml at master · LessUp/micos-2024 · GitHub

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name: micos-2024
channels:
  - conda-forge
  - bioconda
  - defaults
  - qiime2
  - r

dependencies:
  # Python and core packages
  - python=3.9
  - pip
  - numpy
  - pandas
  - scipy
  - matplotlib
  - seaborn
  - plotly
  - jupyter
  - notebook

  # Bioinformatics tools
  - fastqc=0.11.9
  - multiqc
  - kneaddata=0.12.0
  - kraken2=2.1.3
  - krona=2.8.1
  - biom-format
  - qiime2=2024.5

  # R and R packages
  - r-base=4.3.0
  - r-essentials
  - r-devtools
  - r-ggplot2
  - r-dplyr
  - r-tidyr
  - r-readr
  - r-stringr
  - r-plotly
  - r-dt
  - r-shiny
  - r-shinydashboard
  - r-rmarkdown
  - r-knitr
  - bioconductor-phyloseq
  - bioconductor-deseq2
  - bioconductor-biomformat
  - bioconductor-microbiome
  - bioconductor-aldex2
  - bioconductor-ancombc
  - bioconductor-edger
  - bioconductor-limma
  - r-vegan
  - r-ape
  - r-phangorn
  - r-ggtree
  - r-igraph
  - r-corrplot

  # Workflow management
  - cromwell
  - nextflow
  - snakemake

  # Container tools
  - docker-py
  - singularity

  # Additional bioinformatics tools
  - muscle
  - fasttree
  - mafft
  - salmon
  - kallisto
  - diamond
  - blast
  - hmmer
  - prodigal

  # Additional utilities
  - wget
  - curl
  - git
  - parallel
  - pigz
  - samtools
  - bedtools

  # Python packages via pip
  - pip:
    - kraken-biom==1.2.0
    - biopython
    - scikit-learn
    - umap-learn
    - networkx
    - python-louvain
    - community
    - dash
    - dash-bootstrap-components
    - plotly-dash
    - streamlit
    - bokeh
    - altair
    - pyyaml
    - click
    - tqdm
    - joblib
    - psutil
    - memory-profiler
    - line-profiler
    - ete3
    - dendropy
    - skbio
    - qiime2
    - dada2
    - phyloseq
    - deseq2
    - aldex2
    - ancom