environment.yml

# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
name: nf-core-metapep-1.0dev
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - conda-forge::python=3.7.3
  - conda-forge::markdown=3.1.1
  - conda-forge::pymdown-extensions=6.0
  - conda-forge::pygments=2.5.2
  - conda-forge::pandas=1.1.4
  - bioconda::fastqc=0.11.8
  - bioconda::multiqc=1.7
  - conda-forge::biopython=1.78
  - bioconda::prodigal=2.6.3
  - conda-forge::tqdm=4.55.1
# epytope / FRED-2 core dependencies:
  - bioconda::svmlight=6.02
  - conda-forge::coincbc=2.10.5
  - conda-forge::keras=2.3.1
  - bioconda::csvtk=0.21.0
  - conda-forge::pip=20.3.3
  - pip:
    - h5py==2.10.0
    - joblib==1.0.0
    - mhcflurry==1.4.3
    - mhcnames==0.4.8
    - mhcnuggets==2.3.3
    - np-utils==0.5.12.1
    - numpy==1.18.5
    - opt-einsum==3.3.0
    - ply==3.11
    - pymysql==0.10.1
    - pyomo==5.7.2
    - pyutilib==6.0.0
    - pyvcf==0.6.8
    - scikit-learn==0.24.0
    - tensorboard==1.15.0
    - tensorflow==1.15.4
    - tensorflow-estimator==1.15.1
    - threadpoolctl==2.1.0
    - tqdm==4.55.1
# R packages
  - conda-forge::r-ggplot2=3.3.3
  - conda-forge::r-r.utils=2.10.1
  - conda-forge::r-argparser=0.6
  - conda-forge::r-data.table=1.13.6
  - conda-forge::r-tidyverse=1.3.0