diff --git a/EM/EMAN/build b/EM/EMAN/build new file mode 100755 index 0000000..e72e4e4 --- /dev/null +++ b/EM/EMAN/build @@ -0,0 +1,23 @@ +#!/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() { + : +} + +pbuild::install() { + : +} + +pbuild::compile() { + bash ${PMODULES_TMPDIR:-/tmp}/eman${V}_sphire1.4_sparx.linux64.sh -u -b -p $PREFIX +} diff --git a/EM/EMAN/files/variants b/EM/EMAN/files/variants new file mode 100644 index 0000000..f50340f --- /dev/null +++ b/EM/EMAN/files/variants @@ -0,0 +1,2 @@ +EMAN/2.99.47 unstable cuda/11.2.2 +EMAN/2.2 stable diff --git a/EM/EMAN/modulefile b/EM/EMAN/modulefile new file mode 100644 index 0000000..ae15052 --- /dev/null +++ b/EM/EMAN/modulefile @@ -0,0 +1,37 @@ +#%Module1.0 + +set dont-setenv {LD_LIBRARY_PATH} + +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 " + +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. + +Please also note that this is not the (related) EMEN2 electronic notebook, but is EMAN2, a scientific image processing suite. + +Please Cite (and read) + +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 +"