assembly_env.yml

#mamba env create -p path/to/env/ -f assembly_env.yml 
name: assembly_env
channels:
  - anaconda
  - conda-forge
  - bioconda
dependencies:
  - wget=1.21.4
  - make=4.3
  - cmake=3.28.3
  - minimap2=2.28
  - samtools=1.20
  - bcftools
  - flye=2.9.4
  - hifiasm=0.19.9
  - quast=5.2.0
  - merqury=1.3
  - bedtools=2.31.1
  - dgenies=1.5.0
  - genomescope2
  - blast=2.15.0
  - ncbi-genome-download
  - chopper=0.8.0
  - fastp=0.23.4
  - bwa-mem2=2.2.1
  - pilon=1.24
  - canu=2.2
  - pbtk=3.1.1
  - raven-assembler=1.8.3
  - shasta=0.12.0
  - compleasm=0.2.6
    # - r=4.4
  - r-ggplot2=3.5.1
    #  - r-data.table=1.15.4
  - r-ggforce=0.4.2
  - r-dplyr=1.1.4
  - pandas
  - compleasm
  - busco=5.7.1
  - pip=24.2
  - pip:
      - medaka==1.12.1