From 792a562c57d68fda1ffc588737cb2bbd336d1bda Mon Sep 17 00:00:00 2001
From: Spencer Bliven <spencer.bliven@psi.ch>
Date: Tue, 27 Oct 2020 11:42:17 +0100
Subject: [PATCH] Add new 'topaz' environment for EM

---
 .../2019.07/conda-env-defs/topaz/README.md    | 19 +++++++++++++++++++
 .../2019.07/conda-env-defs/topaz/topaz.yml    | 10 ++++++++++
 2 files changed, 29 insertions(+)
 create mode 100644 Programming/anaconda/2019.07/conda-env-defs/topaz/README.md
 create mode 100644 Programming/anaconda/2019.07/conda-env-defs/topaz/topaz.yml

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
+