base-hpc.yml

name: base
channels:
  - conda-forge
  - bioconda
dependencies:
## TOOLS
  - mamba # faster conda
  - pip
#  - mawk=1.3.4 # faster awk (default in Ubuntu)
  - gawk # featurefull awk
  - miller # data processor
  - csvtk
  - xsv
  - visidata
  - pigz # parallel gzip
  - parallel
  - tmux
  - micro # text editor
  - xsel # clipboard for micro
  - visidata # spreadsheet processor
  - bpytop # htop, but awesome
## BIO
  - seqmagick
  - bioawk
  - fastqc
  - samtools
  - bcftools
  - freebayes
  - vcflib
  - plink
  - plink2 # yes, both, totally!
  - tabix
  - grabix
  - seqtk
  - seqkit
## R
  - r-base=4
#  - r-essentials # includes jupyter
  - r-tidyverse
  - r-future # parallel programming
  - r-future.apply
  - r-furrr
  - r-ape
  - r-seqinr
  - r-vcfr
  - radian # Julia/Jupyter style CLI