Commit 186d4b65 authored by bliven_s's avatar bliven_s

Merge branch 'relion' into 'master'

Add relion build script.

See merge request Pmodules/buildblocks!64
parents 45310b1c 8190b0a6
# Relion
## Installation
Relion is installed from git. The ./build script should work for both stable
(tags) and unstable (branches) versions.
Currently only gcc/7.4.0 is used. Better performance is reported with
intel icc and MKL, but this would require additional openmpi variants.
#!/usr/bin/env modbuild
pbuild::add_to_group 'EM'
pbuild::use_cmake
pbuild::prep() {
local BRANCH
if [[ "$V" =~ beta$ ]]; then
BRANCH="ver${V_MAJOR}.${V_MINOR}"
else
BRANCH="${V_PKG}"
fi
git clone --depth=1 -b "$BRANCH" https://github.com/3dem/relion.git "$SRC_DIR" || return $?
}
pbuild::pre_configure() {
pbuild::add_configure_args FORCE_OWN_FFTW=ON
pbuild::add_configure_args FORCE_OWN_FLTK=ON
pbuild::add_configure_args CUDA=ON
pbuild::add_configure_args CudaTexture=ON
pbuild::add_configure_args ALTCPU=ON
pbuild::add_configure_args FORCE_OWN_TBB=ON
# Requires intel compiler
#pbuild::add_configure_args MKLFFT=ON
}
relion/2.1.b1 stable gcc/4.9.4 openmpi/2.0.1 cuda/8.0.44
relion/3.0_beta stable gcc/4.9.4 openmpi/2.0.1 cuda/8.0.44
relion/3.0.8 unstable gcc/7.4.0 openmpi/3.1.4_merlin6 cuda/9.2.148 b:cmake/3.14.0 b:tiff/4.0.9
relion/3.1-beta unstable gcc/7.4.0 openmpi/3.1.4_merlin6 cuda/9.2.148 b:cmake/3.14.0 b:tiff/4.0.9
#%Module1.0
module-whatis "3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM)"
module-url "https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page"
module-license "GPLv2 license"
module-maintainer "Spencer Bliven <spencer.bliven@psi.ch>"
module-help "
RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a
stand-alone computer program that employs an empirical Bayesian approach to
refinement of (multiple) 3D reconstructions or 2D class averages in electron
cryo-microscopy (cryo-EM). It is developed in the group of Sjors Scheres at the
MRC Laboratory of Molecular Biology. Briefly, the ill-posed problem of
3D-reconstruction is regularised by incorporating prior knowledge: the fact
that macromolecular structures are smooth, i.e. they have limited power in the
Fourier domain. In the corresponding Bayesian framework, many parameters of a
statistical model are learned from the data, which leads to objective and
high-quality results without the need for user expertise. The underlying theory
is given in Scheres (2012) JMB. A more detailed description of its
implementation is given in Scheres (2012) JSB. If RELION is useful in your
work, please cite at least one of these papers.
Scheres(2012) JMB http://www.sciencedirect.com/science/article/pii/S0022283611012290
Scheres(2012) JSB http://www.sciencedirect.com/science/article/pii/S1047847712002481
"
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