diff --git a/Programming/anaconda/2019.07/conda-env-defs/topaz/README.md b/Programming/anaconda/2019.07/conda-env-defs/topaz/README.md new file mode 100644 index 0000000..784dea0 --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/topaz/README.md @@ -0,0 +1,19 @@ +# 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. + diff --git a/Programming/anaconda/2019.07/conda-env-defs/topaz/topaz.yml b/Programming/anaconda/2019.07/conda-env-defs/topaz/topaz.yml new file mode 100644 index 0000000..5edabd3 --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/topaz/topaz.yml @@ -0,0 +1,10 @@ +name: topaz-0.2.5 +channels: + - tbepler + - defaults +dependencies: + - python=3.6 + - cudatoolkit=9.2 + - pytorch + - topaz +