From 4e437aefde40522b36433b1812519bca5c015b50 Mon Sep 17 00:00:00 2001
From: Spencer Bliven <spencer.bliven@psi.ch>
Date: Thu, 3 Nov 2022 13:11:32 +0100
Subject: [PATCH] Install IMOD/4.11.20

This is the first version to use modbuild; IMOD/4.9.5 was installed
manually.
---
 EM/IMOD/README.md      | 14 +++++++++++++
 EM/IMOD/build          | 43 ++++++++++++++++++++++++++++++++++++++++
 EM/IMOD/files/variants |  2 ++
 EM/IMOD/modulefile     | 45 ++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 104 insertions(+)
 create mode 100644 EM/IMOD/README.md
 create mode 100755 EM/IMOD/build
 create mode 100644 EM/IMOD/files/variants
 create mode 100644 EM/IMOD/modulefile

diff --git a/EM/IMOD/README.md b/EM/IMOD/README.md
new file mode 100644
index 0000000..034c88d
--- /dev/null
+++ b/EM/IMOD/README.md
@@ -0,0 +1,14 @@
+# 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).
diff --git a/EM/IMOD/build b/EM/IMOD/build
new file mode 100755
index 0000000..a8940a8
--- /dev/null
+++ b/EM/IMOD/build
@@ -0,0 +1,43 @@
+#!/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"
+
+}
+
diff --git a/EM/IMOD/files/variants b/EM/IMOD/files/variants
new file mode 100644
index 0000000..196b2cd
--- /dev/null
+++ b/EM/IMOD/files/variants
@@ -0,0 +1,2 @@
+IMOD/4.9.5	stable	
+IMOD/4.11.20	unstable	cuda/10.1.105
diff --git a/EM/IMOD/modulefile b/EM/IMOD/modulefile
new file mode 100644
index 0000000..d19b9e2
--- /dev/null
+++ b/EM/IMOD/modulefile
@@ -0,0 +1,45 @@
+#%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
+    }
+}