From 832a41da1442cd10884b84c41a8c4ce229d4b05f Mon Sep 17 00:00:00 2001
From: Spencer Bliven <spencer.bliven@psi.ch>
Date: Thu, 6 Oct 2022 16:39:04 +0200
Subject: [PATCH] Create cryoDRGN conda environment

---
 .../2019.07/conda-env-defs/cryodrgn/README.md | 40 +++++++++++++++++++
 .../conda-env-defs/cryodrgn/cryodrgn.yml      | 20 ++++++++++
 2 files changed, 60 insertions(+)
 create mode 100644 Programming/anaconda/2019.07/conda-env-defs/cryodrgn/README.md
 create mode 100644 Programming/anaconda/2019.07/conda-env-defs/cryodrgn/cryodrgn.yml

diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryodrgn/README.md b/Programming/anaconda/2019.07/conda-env-defs/cryodrgn/README.md
new file mode 100644
index 0000000..059d76b
--- /dev/null
+++ b/Programming/anaconda/2019.07/conda-env-defs/cryodrgn/README.md
@@ -0,0 +1,40 @@
+# INSTALLATION
+
+IMPORTANT! DON'T INSTALL WITH AURISTOR. Use an OpenAFS system (e.g. *pmod7*).
+GLIBC>=2.14 is required (so pmod6 doesn't work).
+
+In theory, the yaml environment contains all the requirements. This should be
+updated for each version to change the env name and update requirements.
+
+    CONDA_COPY_ALWAYS=1 conda env create --file cryodrgn.yml
+    conda activate cryodrgn-1.1.0
+
+In practice, some manual installation was required following the github
+instructions. (Most errors ultimately stemed from quota issues, so try the
+file-based install next version).
+
+Now configure jupyterlab:
+
+    jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build
+    jupyter labextension install jupyterlab-plotly --no-build
+    jupyter labextension install plotlywidget --no-build
+    jupyter lab build
+
+## Pmodules
+
+After installing a new environment, wrap it in the EM/cryodrgn module
+
+## Testing
+
+To test:
+
+    conda activate cryodrgn-1.1.0
+    cryodrgn -h
+
+    git clone https://github.com/zhonge/cryodrgn.git
+    cd cryodrgn/testing
+    ./quicktest.sh
+
+It should take ~20 seconds to run and reach a final loss around 0.08 in version
+1.0 and 0.03 in version 1.1+. Note that the output should contain  Use cuda
+True in the first few lines.
diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryodrgn/cryodrgn.yml b/Programming/anaconda/2019.07/conda-env-defs/cryodrgn/cryodrgn.yml
new file mode 100644
index 0000000..95a1373
--- /dev/null
+++ b/Programming/anaconda/2019.07/conda-env-defs/cryodrgn/cryodrgn.yml
@@ -0,0 +1,20 @@
+name: cryodrgn-1.1.0
+channels:
+  - pytorch
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - pytorch
+  - pandas
+  - seaborn
+  - scikit-learn
+  - umap-learn
+  - jupyterlab
+  - ipywidgets
+  - cufflinks-py
+  - nodejs>=15.12.0
+
+  - pip
+  - pip:
+    - git+https://github.com/zhonge/cryodrgn.git@1.1.0