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[DO NOT MERGE] #9045

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[DO NOT MERGE] #9045

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9ca31cb
first attempt at a changed environment
Nov 12, 2024
1cf15f9
updating pytorch to newer version that carries some risk
Nov 15, 2024
10acfbd
gore
Nov 15, 2024
2cf671b
back to basics
Nov 15, 2024
0eeb8b6
uncommenting some
Nov 15, 2024
6be3e4d
trying two more dependencies
Nov 15, 2024
a0e5dbb
enabling two more
Nov 15, 2024
966333d
was it cyvcf?
Nov 18, 2024
090dfef
mmninga?
Nov 18, 2024
c4ed905
another minor alteration of python environment
Nov 19, 2024
788f442
bioconda cyvcf2 is probably a conflict
Nov 19, 2024
e99aeee
bioconda cyvcf2 is probably a conflict
Nov 19, 2024
edba11b
Reverting to 2.1.0
Dec 4, 2024
701fc34
trying to bundle the cuda installation via conda
Dec 9, 2024
9a81630
pairing up the correct cuda compatable pytroch version
Dec 9, 2024
265eafc
change the channel
Dec 9, 2024
49221aa
testing with only cuda backend?
Dec 9, 2024
bf01960
change the channel
Dec 9, 2024
b953413
testing if the other mkl invocation was the problem
Dec 10, 2024
bfefb7b
testing if the other mkl invocation was the problem
Dec 10, 2024
ca5809f
finally! python has lead us from gods light
Dec 10, 2024
4235198
finally! python has lead us from gods light
Dec 10, 2024
684d0ea
this should probably work
Dec 10, 2024
8d66d26
put the code in the right place, now need to build a pythonscriptexec…
Dec 19, 2024
5914af0
hopefully what is needed for docker building proper
Jan 10, 2025
1b66e04
did this really stop working?
Jan 10, 2025
102a225
python installation is dizzying
Jan 10, 2025
1d685a2
moving the cuda drivers into the right stage of the build
Jan 10, 2025
705b5e0
names have power
Jan 13, 2025
094b42e
fixing a silly mistake
Jan 13, 2025
578c7b1
made a somewhat robust mechanism for converting to the python argumen…
Jan 15, 2025
7e85678
some more script editing
Jan 16, 2025
d9f9c40
some more script editing
Jan 16, 2025
aaee681
added the next few tasks from the main wdl
Jan 17, 2025
15644f2
added the next few tasks from the main wdl
Jan 17, 2025
36ae7f2
added docstore bindings to the permutect wdls
Jan 21, 2025
f78d4a1
maybe the branches are the problem
Jan 21, 2025
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11 changes: 9 additions & 2 deletions scripts/gatkcondaenv.yml.template
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Expand Up @@ -29,14 +29,21 @@ dependencies:
- 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=2.3.0=*mkl*100
- conda-forge::pytorch-lightning=2.4.0 # supports Pytorch >= 2.1 and <= 2.4, used by NVScoreVariants
- conda-forge::tensorboard=2.8.0
- 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
- conda-forge::setuptools>=57.0.0
- conda-forge::psutil>=5.9.2
- conda-forge::protobuf<3.20,>=3.9.2 # Protobuf constraint for TensorFlow compatibility
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Didn't we get rid of tensorflow?

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@jamesemery jamesemery Nov 15, 2024 •
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No idea. Its in the dependencies for the other project:

# Protobuf 4.0 is incompatible with TF. Force < 3.20 until they unblock upgrade.
# See: http://b/182876485
# See: https://github.com/protocolbuffers/protobuf/issues/9954#issuecomment-1128283911
# See: https://cs.opensource.google/tensorflow/tensorflow/+/master:tensorflow/tools/pip_package/setup.py?q=protobuf
protobuf >= 3.9.2, < 3.20

- conda-forge::intervaltree~=3.1.0
- conda-forge::cyvcf2~=0.30.15
- conda-forge::mmap-ninja>=0.2.4

# core R dependencies; these should only be used for plotting and do not take precedence over core python dependencies!
- r-base=4.3.1
Expand All @@ -55,4 +62,4 @@ dependencies:

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