Commit 6d5404c2 authored by bliven_s's avatar bliven_s

Merge branch 'topaz' into 'master'

Add new 'topaz' environment for EM

See merge request Pmodules/buildblocks!129
parents f695b5b6 792a562c
# 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.
name: topaz-0.2.5
channels:
- tbepler
- defaults
dependencies:
- python=3.6
- cudatoolkit=9.2
- pytorch
- topaz
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