Commit 052151c0 authored by bliven_s's avatar bliven_s
Browse files

Create cryodrgn pmodule

Wraps the conda environment
parent 832a41da
# 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
#!/usr/bin/env modbuild
pbuild::add_to_group 'EM'
pbuild::prep() {
:
}
pbuild::configure() {
:
}
pbuild::compile() {
:
}
pbuild::install() {
:
}
cryodrgn/1.1.0 stable anaconda/2019.07
#%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"
}
}
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