environment.yml

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##   environment.yml
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##   Defining conda/mamba software dependencies to run CAPTVRED pipeline for capture-based viral metagneomics.
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##
##    CopyLeft 2024 (CC:BY-NC-SA) --- Maria Tarrdas-Alemany & Josep F Abril
##
##   This file should be considered under the Creative Commons BY-NC-SA License
##   (Attribution-Noncommercial-ShareAlike). The material is provided and distributed 
##   in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the 
##   implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
##
## ######################################################################################
#
# To install software ensure you have conda installed and use the following command:
#
#    conda env create --file environment.yml
# 
# then run the command below to activate the conda environment:
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#    conda activate captvred
#
name: captvred
channels:
  - bioconda
  - r
  - conda-forge
  - defaults
dependencies: 
  - nextflow=22.04
  - perl
  - perl-bioperl
  - perl-yaml
  - python=3.9.2
  - biopython
  - pandas
  - bbmap
  - fastqc
  - multiqc=1.9
  - bowtie2
  - samtools
  - seqkit
  - megahit
  - spades
  - blast
  - gawk
  - kaiju=1.9.0
  # R-packages
  - r-base=4.0.5
  - r-ggplot2
  - r-tidyverse
  - r-plyr
  - r-gridExtra
  - bioconductor-rtracklayer
  #- bioconductor-GenomicFeatures=1.42.3
  - bioconductor-Rsamtools
  - bioconductor-GenomicAlignments
  - bioconductor-VariantAnnotation
  - bioconductor-ggbio