Merge branch 'cryodrgn' into 'master'

Create cryodrgn/1.1.0 pmodule

See merge request Pmodules/buildblocks!354

EM/cryodrgn/README.md

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+# cryoDRGN
+
+CryoDRGN is installed in a central conda environment. 
+## Adding New Versions
+
+To add a new version, first create the conda environment, as described in
+../../Programming/anaconda/2019.07/conda-env-defs/cryodrgn/README.md.
+
+Next, update files/variants with the new version and run `./build <VERSION>` to
+install the modulefile
+

EM/cryodrgn/build

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+#!/usr/bin/env modbuild
+
+
+pbuild::add_to_group 'EM'
+pbuild::prep() {
+    :
+}
+
+pbuild::configure() {
+    :
+}
+
+pbuild::compile() {
+    :
+}
+
+pbuild::install() {
+    :
+}
+

EM/cryodrgn/files/variants

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+cryodrgn/1.1.0	stable	anaconda/2019.07
+

EM/cryodrgn/modulefile

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+#%Module
+
+module-whatis           "cryoDRGN: Deep Reconstructing Generative Networks for cryo-EM heterogeneous reconstruction"
+module-url              "https://github.com/zhonge/cryodrgn"
+module-license          "GPL v3.0"
+module-maintainer       "Spencer Bliven <spencer.bliven@psi.ch>"
+
+module-help     "
+CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM
+reconstruction. In particular, the method models a continuous distribution over
+3D structures by using a neural network based representation for the volume.
+
+> CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural
+> networks. Ellen D. Zhong, Tristan Bepler, Bonnie Berger, Joseph H. Davis.
+> https://www.nature.com/articles/s41592-020-01049-4
+
+> Reconstructing continuous distributions of 3D protein structure from cryo-EM
+> images. Ellen D. Zhong, Tristan Bepler, Joseph H. Davis, Bonnie Berger.
+> ICLR 2020, Spotlight presentation, https://arxiv.org/abs/1909.05215
+"
+
+# Check for supported shell types
+set shelltype [module-info shelltype]
+switch -- $shelltype {
+    "sh" {
+        puts stdout "source \"\${ANACONDA_PREFIX}\"/admintools/conda_setup.sh;\n"
+    }
+    default {
+        puts stderr "Shells of type '$shelltype' are NOT supported!"
+    }
+}
+
+# Determine useflags and construct conda env name
+set list [split $V "_"]
+set version  [lindex ${list} 0]
+set useflags [lrange ${list} 1 end]
+set env_to_activate [string tolower ${P}]-${version}
+
+switch [module-info mode] {
+    "load" {
+      # Relies on the anaconda module being loaded since we need to update the path
+      puts stdout "conda activate $env_to_activate;\n"
+    }
+    "unload" -
+    "remove" {
+        puts stdout "conda deactivate;\n"
+    }
+}
+

Programming/anaconda/2019.07/conda-env-defs/cryodrgn/README.md

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+# 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.

Programming/anaconda/2019.07/conda-env-defs/cryodrgn/cryodrgn.yml

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+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