python 3.10.9, pymc3 3.11.2

scripts/gatkcondaenv.yml.template

@@ -10,51 +10,42 @@
 # used by the testGATKPythonEnvironmentPackagePresent test in PythonEnvironmentIntegrationTest needs to be updated
 # to reflect the changes.
 #
-name: $condaEnvName
+name: gatk
 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 and compiled against MKL
 - conda-forge
-- defaults
 dependencies:
 
 # core python dependencies
-- conda-forge::python=3.10          # do not update without good reason
-- pip=20.0.2                        # specifying channel may cause a warning to be emitted by conda
-- conda-forge::mkl=2022.1.0         # MKL typically provides dramatic performance increases for theano, tensorflow, and other key dependencies
+- conda-forge::python=3.10.9        # do not update without good reason
+- pip                               # specifying channel may cause a warning to be emitted by conda
+- conda-forge::mkl=2022.2.1
 - conda-forge::mkl-service=2.4.0
-- conda-forge::numpy=1.21.2         # verify that numpy is compiled against MKL (e.g., by checking *_mkl_info using numpy.show_config())
+- conda-forge::numpy=1.26.0         # verify that numpy is compiled against MKL (e.g., by checking *_mkl_info using numpy.show_config())
                                     #   and that it is used in tensorflow, theano, and other key dependencies
-- conda-forge::theano=1.0.5         # it is unlikely that new versions of theano will be released
                                     #   verify that this is using numpy compiled against MKL (e.g., by the presence of -lmkl_rt in theano.config.blas.ldflags)
-- conda-forge::pymc3=3.5            # do not update without goodreason, this may break gcnvkernel
-- conda-forge::scipy=1.5.3
-- conda-forge::h5py=3.1.0           # newer versions produce an import issue https://github.com/h5py/h5py/issues/1880
-- conda-forge::pytorch=1.10.1
+- conda-forge::pymc3=3.11.2         # do not update without good reason, this may break gcnvkernel
+- conda-forge::theano-pymc=1.1.2    # do not update without good reason, this may break gcnvkernel
+- conda-forge::scipy=1.7.3
+- conda-forge::h5py=3.10.0
+- conda-forge::pytorch=2.0.0
 
-- defaults::intel-openmp=2021.4.0
-- conda-forge::scikit-learn=0.23.1
-- conda-forge::matplotlib=3.2.1
-- conda-forge::pandas=1.0.3
-- conda-forge::typing_extensions=4.1.1   # see https://github.com/broadinstitute/gatk/issues/7800 and linked PRs
-- conda-forge::dill=0.3.4                # used for pickling lambdas in TrainVariantAnnotationsModel
-- conda-forge::setuptools=59.5.0
+- conda-forge::scikit-learn=1.3.1
+- conda-forge::matplotlib=3.9.0
+- conda-forge::pandas=2.1.1
+- conda-forge::dill=0.3.7                 # used for pickling lambdas in TrainVariantAnnotationsModel
 
 
-#other python dependencies; these should be removed after functionality is moved into Java code
-- biopython=1.76
-- pyvcf=0.6.8
-- bioconda::pysam=0.15.3            # using older conda-installed versions may result in libcrypto / openssl bugs
-
-- r-base=3.6.2
-- r-data.table=1.12.8
-- r-dplyr=0.8.5
-- r-getopt=1.20.3
-- r-ggplot2=3.3.0
-- r-gplots=3.0.3
-- r-gsalib=2.1
-- r-optparse=1.6.4
-- r-backports=1.1.10
+- 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
 
 # pip installs should be avoided, as pip may not respect the dependencies found by the conda solver
 - pip: