diff --git a/EM/relion/build b/EM/relion/build new file mode 100755 index 0000000..720a59f --- /dev/null +++ b/EM/relion/build @@ -0,0 +1,28 @@ +#!/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 +} + diff --git a/EM/relion/files/variants b/EM/relion/files/variants new file mode 100644 index 0000000..34ef8b8 --- /dev/null +++ b/EM/relion/files/variants @@ -0,0 +1,5 @@ +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 + diff --git a/EM/relion/modulefile b/EM/relion/modulefile new file mode 100644 index 0000000..d42d775 --- /dev/null +++ b/EM/relion/modulefile @@ -0,0 +1,27 @@ +#%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 " + +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 +" + +