lsaBGC_env.yml

name: lsaBGC
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - python>=3.9
  - setuptools<=58.2.0
  - pip=22.1.2
  - conda-forge::cxx-compiler
  - biopython=1.79
  - pysam=0.16.0.1
  - bioconda::bowtie2=2.4.5
  - bioconda::samtools=1.12
  - bioconda::mafft=7.505
  - bioconda::mcl=14.137
  - bioconda::pal2nal=14.1
  - bioconda::hmmer=3.3.2
  - bioconda::orthofinder=2.5.4
  - bioconda::panaroo
  - bioconda::fasttree=2.1.11
  - conda-forge::ete3=3.1.2
  - bioconda::diamond=2.0.15
  - r-base
  - r-ggplot2
  - r-cowplot
  - r-phytools
  - r-ape
  - r-scatterpie
  - r-dplyr
  - r-gggenes
  - bioconductor-ggtree
  - r-ggalluvial
  - r-data.table
  - r-plyr
  - r-gridextra
  - bioconda::prodigal
  - bioconda::pyrodigal=2.3.0
  - conda-forge::tar
  - conda-forge::pandas
  - conda-forge::pomegranate=0.13.3
  - bioconda::mash
  - bioconda::gtotree
  - conda-forge::xlsxwriter=3.0.3
  - bioconda::ncbi-genome-download
  - bioconda::gecco
  - bioconda::n50
  - conda-forge::networkx
  - scipy
  - scikit-learn
  - numpy