Add new 'topaz' environment for EM

2020-10-27 11:48:05 +01:00
parent 832c480846
commit 792a562c57
2 changed files with 29 additions and 0 deletions
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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.
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 name: topaz-0.2.5
 channels:
  - tbepler
  - defaults
 dependencies:
  - python=3.6
  - cudatoolkit=9.2
  - pytorch
  - topaz