environment.yml

# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
name: predector
channels:
  - predector
  - darcyabjones
  - conda-forge
  - bioconda
dependencies:
  ## Python 3.10 doesn't work yet, a few packages haven't been built yet.
  - conda-forge::python=3.9
  ## Custom packages
  - predector::apoplastp=1.0.1
  - predector::deeploc=1.0=h6bb024c_3
  - predector::deepsig=0f1e1d9=2
  - predector::effectorp1=1.0
  - predector::effectorp2=2.0
  - predector::effectorp3=3.0=py_2
  - predector::localizer=1.0.4
  - predector::phobius=1.01=4
  - predector::predectorutils=0.9.0
  - predector::signalp3=3.0b=3
  - predector::signalp4=4.1g=3
  - predector::signalp5=5.0b=2
  - predector::signalp6=6.0g=1
  - predector::targetp2=2.0=2
  - predector::tmhmm=2.0c=3
  - predector::deepredeff-py=0.0.1
  ## Conda-forge packages
  - conda-forge::gawk
  - conda-forge::gzip
  - conda-forge::wget
  - conda-forge::parallel
  - tensorflow=2.7=cpu*
  - conda-forge::keras=2.7
  - conda-forge::numpy>=1.22
  - conda-forge::xz
  - conda-forge::zlib
  - conda-forge::bzip2
  ## some versions of moose install for different versions of perl than the one you're targeting
  ## make sure you pin the versions and check
  ## moose needed for pfamscan
  - bioconda::perl-moose=2.2011
  - conda-forge::perl=5.26.2
  ## Bioconda packages
  - bioconda::emboss=6.6.0
  - bioconda::hmmer=3.3.2
  - bioconda::pfam_scan=1.6
  - bioconda::mmseqs2>=13.45111
  ## Version pins that aren't completely necessary but make solving environment faster
  - conda-forge::pytorch-cpu=1.11
  - conda-forge::sqlite>=3.38
  - conda-forge::openjdk>=11
  - conda-forge::theano=1.0.5
  - pip
  - pip:
    - importlib-resources