environment.yml

## Environment file to reproduce exercises
name: pgip
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - bash_kernel
  - bedtools
  - bcftools
  - bokeh
  - bwa
  - ca-certificates
  - csvtk
  - cyvcf2=0.30.16
  - demesdraw
  - d4tools
  - fastqc
  - gatk4
  - gawk
  - htslib=1.15.1
  - jupyter
  - jupyter-cache
  - mosdepth=0.3.3
  - msprime>=1.2
  - multiqc
  - pandas
  - pip
  - picard<3
  - pyslim
  - python>=3.10
  - python-newick
  - qualimap
  - r-ape
  - r-codetools
  - r-curl
  - r-devtools
  - r-dt
  - r-dygraphs
  - r-expm
  - r-fontawesome
  - r-formatr
  - r-formattable
  - r-gganimate
  - r-ggiraph
  - r-ggraph
  - r-ggplot2
  - r-gifski
  - r-gplots
  - r-gsalib
  - r-highcharter
  - r-igraph
  - r-kableextra
  - r-latex2exp
  - r-leaflet
  - r-networkD3
  - r-magick
  - r-patchwork
  - r-pdftools
  - r-plotly
  - r-readr
  - r-readxl
  - r-reticulate
  - r-rmarkdown>=2.19
  - r-tidyr
  - r-viridis
  - samtools=1.15.1
  - scikit-allel
  - seqkit
  - slim>=4.0
  - sgkit
  - tskit>=0.5.0
  - vcflib=1.0.1
  - vcftools