Merge branch '308-eman_2-99-66' into 'master'
Resolve "eman_2.99.66" Closes #308 See merge request Pmodules/buildblocks!475
This commit is contained in:
10
EM/EMAN/README.md
Normal file
10
EM/EMAN/README.md
Normal file
@@ -0,0 +1,10 @@
|
||||
# EMAN
|
||||
|
||||
From version 2.99.53 (Oct. 23) EMAN is built as a conda package.
|
||||
|
||||
Current installation on Merlin7 (Nov 24) is 2.99.66
|
||||
|
||||
|
||||
### Hints
|
||||
|
||||
conda installation on A100 GPU
|
||||
@@ -1,23 +1,27 @@
|
||||
#!/usr/bin/env modbuild
|
||||
|
||||
pbuild::add_to_group 'EM'
|
||||
|
||||
pbuild::prep() {
|
||||
local EMAN2DL="${PMODULES_TMPDIR:-/tmp}/eman${V}_sphire1.4_sparx.linux64.sh"
|
||||
|
||||
if ! [ -f "$EMAN2DL" ]; then
|
||||
wget -O "$EMAN2DL" "https://cryoem.bcm.edu/cryoem/static/software/release-${V}/eman${V}_sphire1.4_sparx.linux64.sh"
|
||||
fi
|
||||
}
|
||||
|
||||
pbuild::configure() {
|
||||
#MINICONDA INSTALL
|
||||
mkdir -p "$PREFIX/miniconda"
|
||||
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O "$PREFIX/miniconda/miniconda.sh"
|
||||
bash "$PREFIX/miniconda/miniconda.sh" -b -u -p "$PREFIX/miniconda/"
|
||||
|
||||
|
||||
#CREATE ENV , make sure to source the "correct" conda.sh
|
||||
"$PREFIX/miniconda/condabin/conda" env create --name "${P}_${V}" -f "$BUILDBLOCK_DIR/environment.yaml"
|
||||
|
||||
}
|
||||
|
||||
#DO NOTHING
|
||||
pbuild::compile(){
|
||||
:
|
||||
}
|
||||
|
||||
pbuild::install() {
|
||||
pbuild::install(){
|
||||
:
|
||||
}
|
||||
|
||||
pbuild::compile() {
|
||||
bash ${PMODULES_TMPDIR:-/tmp}/eman${V}_sphire1.4_sparx.linux64.sh -u -b -p $PREFIX
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
5
EM/EMAN/environment.yaml
Normal file
5
EM/EMAN/environment.yaml
Normal file
@@ -0,0 +1,5 @@
|
||||
channels:
|
||||
- cryoem
|
||||
- conda-forge
|
||||
dependencies:
|
||||
- eman-dev
|
||||
13
EM/EMAN/files/config.yaml
Normal file
13
EM/EMAN/files/config.yaml
Normal file
@@ -0,0 +1,13 @@
|
||||
---
|
||||
format: 1
|
||||
EMAN:
|
||||
defaults:
|
||||
group: EM
|
||||
overlay: base
|
||||
relstage: unstable
|
||||
versions:
|
||||
2.99.66:
|
||||
variants:
|
||||
- overlay: Alps
|
||||
systems: [.*.merlin7.psi.ch]
|
||||
relstage: unstable
|
||||
@@ -1,2 +0,0 @@
|
||||
EMAN/2.99.47 unstable cuda/11.2.2
|
||||
EMAN/2.2 stable
|
||||
@@ -1,37 +1,34 @@
|
||||
#%Module1.0
|
||||
#%Module
|
||||
|
||||
set dont-setenv {LD_LIBRARY_PATH}
|
||||
module-whatis "EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes "
|
||||
module-url "https://blake.bcm.edu/emanwiki/EMAN2"
|
||||
module-license "GNU gerneral public license: GPLv2"
|
||||
module-maintainer "Greta Assmann <greta.assmann@psi.ch>"
|
||||
|
||||
module-whatis "EMAN(2) is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes"
|
||||
module-url "https://blake.bcm.edu/emanwiki/EMAN2"
|
||||
module-license "GPL license"
|
||||
module-maintainer "Elsa Germann <elsa.germann@psi.ch>"
|
||||
module-help "EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing large data sets (>100,000 particle) very efficiently"
|
||||
|
||||
module-help "EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing large data sets (>100,000 particle) very efficiently.
|
||||
# Check for supported shell types
|
||||
set shelltype [module-info shelltype]
|
||||
switch -- $shelltype {
|
||||
"sh" {
|
||||
puts stdout "conda(){ :; };"
|
||||
puts stdout "set +u"
|
||||
puts stdout "source \"${PREFIX}\"/miniconda/etc/profile.d/conda.sh;\n"
|
||||
}
|
||||
default {
|
||||
puts stderr "Shells of type '$shelltype' are NOT supported!"
|
||||
}
|
||||
}
|
||||
|
||||
Please also note that this is not the (related) EMEN2 electronic notebook, but is EMAN2, a scientific image processing suite.
|
||||
|
||||
Please Cite (and read)
|
||||
switch [module-info mode] {
|
||||
"load" {
|
||||
# Relies on the anaconda module being loaded since we need to update the path
|
||||
puts stdout "conda activate ${P}_${V};\n"
|
||||
}
|
||||
"unload" -
|
||||
"remove" {
|
||||
puts stdout "conda deactivate;\n"
|
||||
}
|
||||
}
|
||||
|
||||
EMAN is free software, supported by NIH Grants. It is critical that you cite EMAN2 when you use it in a publication in any significant way, to help us document usage when trying to renew our funding. Feel free to cite any of these:
|
||||
|
||||
Primary EMAN2 paper:
|
||||
|
||||
G. Tang, L. Peng, P.R. Baldwin, D.S. Mann, W. Jiang, I. Rees & S.J. Ludtke. (2007) EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol. 157, 38-46. PMID: 16859925
|
||||
|
||||
Subnanometer resolution subtomogram averaging using PPPT methods:
|
||||
Chen M, Bell JM, Shi X, Sun SY, Wang Z, Ludtke SJ. Nat Methods. (2019) A complete data processing workflow for cryo-ET and subtomogram averaging, Nat. Methods, 16(11):1161-1168, PMC31611690
|
||||
|
||||
Neural Network Based Tomogram Segmentation
|
||||
Chen M, Dai W, Sun SY, Jonasch D, He CY, Schmid MF, et al. (2017). Convolutional neural networks for automated annotation of cellular cryo-electron tomograms. Nat. Methods, 14(10), 983–5. PMCID: PMC5623144
|
||||
|
||||
Neural Network Particle Picker
|
||||
Bell JM, Chen M, Durmaz T, Fluty AC, Ludtke SJ. (2018). New software tools in EMAN2 inspired by EMDatabank map challenge. J. Struct. Biol. Elsevier;, 204(2), 283–90.
|
||||
|
||||
EMAN2 high resolution refinement methods:
|
||||
|
||||
J.M. Bell, M. Chen, P.R. Baldwin & S.J. Ludtke. (2016) High Resolution Single Particle Refinement in EMAN2.1. Methods. 100, 25-34. PMC4848122
|
||||
|
||||
Methods for analysis of conformational and compositional variability:
|
||||
Ludtke, S. J. \"Single-Particle Refinement and Variability Analysis in EMAN2.1.\" in Methods Enzymol 579159-189 (Elsevier, United States, 2016). PMC5101015
|
||||
"
|
||||
|
||||
Reference in New Issue
Block a user