gatkcondaenv.yml.template

# $condaEnvDescription
#
# Only update this environment if there is a *VERY* good reason to do so!
# If the build is broken but could be fixed by doing something else, then do that thing instead.
# Ensuring the correct environment for canonical (or otherwise reasonable) usage of our standard Docker takes precedence over edge cases.
# If you break the environment, you are responsible for fixing it and also owe the last developer who left this in a reasonable state a beverage of their choice.
# (This may be yourself, and you'll appreciate that beverage while you tinker with dependencies!)
#
# When changing dependencies or versions in this file, check to see if the "supportedPythonPackages" DataProvider
# used by the testGATKPythonEnvironmentPackagePresent test in PythonEnvironmentIntegrationTest needs to be updated
# to reflect the changes.
#
# NOTE: If you update any of the packages below, please make sure the main README is up to date with the latest package install information.
#
name: $condaEnvName
channels:
# if channels other than conda-forge are added and the channel order is changed (note that conda channel_priority is currently set to flexible),
# verify that key dependencies are installed from the correct channel
- conda-forge

dependencies:

# core python dependencies
- conda-forge::python=3.10.13         # do not update without good reason
- conda-forge:pip=23.3.1
- conda-forge:blas=1.0=mkl            # our official environment uses MKL versions of various packages; if other versions are desired, users should edit this YML accordingly
- conda-forge::numpy=1.26.2
- conda-forge::pymc=5.10.1
- conda-forge::pytensor=2.18.3
- conda-forge::scipy=1.11.4
- conda-forge::h5py=3.10.0
- conda-forge::pytorch=2.1.0=*mkl*100
- conda-forge::pytorch-lightning=2.4.0   # supports Pytorch >= 2.1 and <= 2.4, used by NVScoreVariants
- conda-forge::scikit-learn=1.3.2
- conda-forge::matplotlib=3.8.2
- conda-forge::pandas=2.1.3
- conda-forge::tqdm=4.66.1
- conda-forge::dill=0.3.7             # used for pickling lambdas in TrainVariantAnnotationsModel
- conda-forge::biopython=1.84         # used by NVScoreVariants

# core R dependencies; these should only be used for plotting and do not take precedence over core python dependencies!
- r-base=4.3.1
- r-data.table=1.14.8
- r-dplyr=1.1.3
- r-getopt=1.20.4
- r-ggplot2=3.4.4
- r-gplots=3.1.3
- r-gsalib=2.2.1
- r-optparse=1.7.3
- r-backports=1.4.1

# other python dependencies; these should be removed after functionality is moved into Java code
- bioconda::pysam=0.22.0
- conda-forge::pyvcf=0.6.8

# pip installs should be avoided, as pip may not respect the dependencies found by the conda solver
- pip:
  - gatkPythonPackageArchive.zip