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buildblocks
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792a562c
Commit
792a562c
authored
Oct 27, 2020
by
bliven_s
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Add new 'topaz' environment for EM
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832c4808
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Programming/anaconda/2019.07/conda-env-defs/topaz/README.md
Programming/anaconda/2019.07/conda-env-defs/topaz/README.md
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Programming/anaconda/2019.07/conda-env-defs/topaz/topaz.yml
Programming/anaconda/2019.07/conda-env-defs/topaz/topaz.yml
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Programming/anaconda/2019.07/conda-env-defs/topaz/README.md
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# Topaz
[
Topaz
](
https://github.com/tbepler/topaz
)
is a conda-based cryoEM particle
picker. It is used primarily through cryosparc, but also provides python
notebooks.
See https://intranet.psi.ch/en/bio/computing-cryosparc
## INSTALLATION
IMPORTANT! DON'T INSTALL WITH AURISTOR. Use an OpenAFS system (e.g. pmod6)
export TMPDIR=/opt/tmp/$USER
export XDG_CACHE_HOME=/opt/tmp/$USER/.cache
CONDA_COPY_ALWAYS=1 conda env create --file topaz.yml
conda activate topaz-0.2.5
The alternate TMPDIR is required on pmod6 because /tmp is too small for pip to expand all wheel files.
Programming/anaconda/2019.07/conda-env-defs/topaz/topaz.yml
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name
:
topaz-0.2.5
channels
:
-
tbepler
-
defaults
dependencies
:
-
python=3.6
-
cudatoolkit=9.2
-
pytorch
-
topaz
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