Commit 4e437aef authored by bliven_s's avatar bliven_s
Browse files

Install IMOD/4.11.20

This is the first version to use modbuild; IMOD/4.9.5 was installed
manually.
parent a09fe1e7
# IMOD
## Installation
IMOD is shipped as a self-expanding installation script. Run `./build` to
install.
## Known Issues
The installation includes environment scripts which install into
`$IMOD_DIR/profile.d`. These are sourced in the modulefile. This means that the
module cannot be unloaded cleanly (eg IMOD remains in the PATH after
unloading).
#!/usr/bin/env modbuild
pbuild::add_to_group 'EM'
pbuild::prep() {
: ${CUDA_VERSION:?No CUDA_VERSION set}
local cuda="${CUDA_VERSION%.*}"
local filename="imod_${V_PKG}_RHEL7-64_CUDA${cuda}.sh"
local dst="$PMODULES_DISTFILESDIR/${filename}"
if [ -f "$dst" ]; then
echo "Found cached $dst" >&2
else
${curl:-curl} \
--location \
--fail \
--output "$dst" \
"https://bio3d.colorado.edu/imod/AMD64-RHEL5/$filename"
fi
}
pbuild::configure() {
:
}
pbuild::compile() {
:
}
pbuild::install() {
: ${CUDA_VERSION:?No CUDA_VERSION set}
local cuda="${CUDA_VERSION%.*}"
local filename="imod_${V_PKG}_RHEL7-64_CUDA${cuda}.sh"
local dst="$PMODULES_DISTFILESDIR/${filename}"
mkdir -p "$PREFIX/profile.d"
sh "$dst" \
-yes \
-dir "$PREFIX" \
-script "$PREFIX/profile.d"
}
IMOD/4.9.5 stable
IMOD/4.11.20 unstable cuda/10.1.105
#%Module1.0
module-whatis "IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections."
module-url "http://bio3d.colorado.edu/imod/"
module-license "mostly GPLv2.0, with the exceptions, see http://bio3d.colorado.edu/imod/COPYRIGHT.txt"
module-maintainer "Spencer Bliven <spencer.bliven@psi.ch> / Dmitry Ozerov <dmitry.ozerov@psi.ch>"
module-help "
IMOD is a set of image processing, modeling and display programs used for tomographic
reconstruction and for 3D reconstruction of EM serial sections and optical sections.
The package contains tools for assembling and aligning data within multiple types and
sizes of image stacks, viewing 3-D data from any orientation, and modeling and display
of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette,
Sue Held, Jim Kremer, Quanren Xiong, and John Heumann at the University of Colorado.
The development of IMOD has been supported by grants from the National Center for
Research Resources, the National Institute of General Medical Sciences, and the National
Institute for Biomedical Imaging and Bioengineering. IMOD and virtually all programs
contained within the IMOD package are Copyright (c) 1994-2017 by the Regents of the
University of Colorado. Other contributors are acknowledged in our Copyright and
Credits statement http://bio3d.colorado.edu/imod/COPYRIGHT.txt.
Original publication:
> Kremer J.R., Mastronarde, D.N., and McIntosh, J.R. (1996) Computer
> visualization of three-dimensional image data using IMOD. J. Struct. Biol.
> 116:71-76.
For tomographic reconstruction, see also:
> Mastronarde, D.N. (1997) Dual-axis tomography: an approach with alignment
> methods that preserve resolution. J. Struct. Biol. 120:343-352.
> Mastronarde, D.N. and Held, S.R. (2017) Automated tilt series alignment and
> tomographic reconstruction in IMOD. J. Struct. Biol. 197:102-113.
"
switch [module-info mode] {
"load" {
puts stdout "source $PREFIX/profile.d/IMOD-linux.sh"
}
"unload" -
"remove" {
# Could unset IMOD variables here
}
}
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment