environment.yml

# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
name: nfcore-smrnaseq-1.0
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - conda-forge::openjdk=8.0.144 # Needed for FastQC - conda build hangs without this
  - fastqc=0.11.7
  - trim-galore=0.5.0
  - samtools=1.9
  - bowtie=1.2.2
  - multiqc=1.7
  - bioconductor-edger=3.20.7
  - bioconductor-limma=3.34.9
  - conda-forge::r-statmod=1.4.30
  - conda-forge::r-data.table=1.11.4
  - conda-forge::r-gplots=3.0.1
  - conda-forge::r-r.methodss3=1.7.1
  - htseq=0.9.1
  - fastx_toolkit=0.0.14
  - mirtrace=1.0.0
  # Install NGI Visualizations
  # TODO: Replace dependency / conda-ise somehow
  - pip:
     - "--editable=git+https://github.com/NationalGenomicsInfrastructure/ngi_visualizations.git#egg=ngi_visualizations"