From 05653093ff45f90637e0104d04ad6882b6a366c9 Mon Sep 17 00:00:00 2001
From: Spencer Bliven <spencer.bliven@psi.ch>
Date: Wed, 12 Oct 2022 16:20:40 +0200
Subject: [PATCH] New module: PEET

---
 EM/PEET/README.md                  | 27 ++++++++++++++++++++
 EM/PEET/build                      | 41 ++++++++++++++++++++++++++++++
 EM/PEET/files/_config.yaml.disable |  8 ++++++
 EM/PEET/files/variants             |  1 +
 EM/PEET/modulefile                 | 30 ++++++++++++++++++++++
 5 files changed, 107 insertions(+)
 create mode 100644 EM/PEET/README.md
 create mode 100755 EM/PEET/build
 create mode 100644 EM/PEET/files/_config.yaml.disable
 create mode 100644 EM/PEET/files/variants
 create mode 100644 EM/PEET/modulefile

diff --git a/EM/PEET/README.md b/EM/PEET/README.md
new file mode 100644
index 0000000..9828d75
--- /dev/null
+++ b/EM/PEET/README.md
@@ -0,0 +1,27 @@
+# PEET
+
+[Particle Estimateion for Electron Tomography](https://bio3d.colorado.edu/PEET/)
+
+## Installation
+
+PEET is shipped as a self-expanding installation script. Run `./build` to
+install.
+
+An experimental config.yaml files is included using Pmodules/1.1.10 syntax.
+This should probably not be used until yaml support in modbuild stabilizes.
+
+## Testing
+
+- `calcFSC` should print the version number
+
+## Build notes
+
+Building was successful with Pmodules 1.1.8 but not 1.1.9 or 1.1.10.
+
+Linking the binary is a bit of a pain. It requires gcc to be loaded to provide
+relatively recent versions of libstdc++.so.6. I didn't fine what exact version
+Matlab MCR expects, but 9.5.0 seemed to work. MCR is linked dynamically at
+runtime through LD_LIBRARY_PATH. This is not set in the modulefile as expected,
+but rather in wrapper scripts which source particle.cfg. Sed commands in
+pbuild::install update this file so that it reads the loaded modules correctly.
+
diff --git a/EM/PEET/build b/EM/PEET/build
new file mode 100755
index 0000000..27d7f66
--- /dev/null
+++ b/EM/PEET/build
@@ -0,0 +1,41 @@
+#!/usr/bin/env modbuild
+
+pbuild::add_to_group 'EM'
+
+
+pbuild::prep() {
+    dst="$PMODULES_DISTFILESDIR/Particle_${V_PKG}_linux.sh"
+    if [ -f "$dst" ]; then
+        echo "Found cached $dst" >&2
+    else
+        ${curl:-curl} \
+            --location \
+            --fail \
+            --output "$dst" \
+            "https://bio3d.colorado.edu/ftp/PEET/linux/Particle_${V_PKG}_linux.sh"
+    fi
+    }
+
+pbuild::configure() {
+    :
+}
+
+pbuild::compile() {
+    :
+}
+
+pbuild::install() {
+    mkdir -p "$PREFIX/etc/profile.d"
+    # Installs into $PREFIX/Particle
+    sh "$PMODULES_DISTFILESDIR/Particle_${V_PKG}_linux.sh" \
+        --yes \
+        --dir "$PREFIX" \
+        --script "$PREFIX/etc/profile.d"
+
+    # Fix paths
+    sed -ri 's,/usr/local/Particle(Runtime)?,$PEET_HOME,g' $PREFIX/Particle/*.{csh,sh,cfg} $PREFIX/etc/profile.d/Particle.{c,}sh
+    sed -ri 's,MCR_ROOT=.*,MCR_ROOT=$MATLAB_DIR,g' $PREFIX/Particle/*.cfg
+
+    mv $PREFIX/Particle/* $PREFIX/
+    rm -r $PREFIX/Particle
+}
diff --git a/EM/PEET/files/_config.yaml.disable b/EM/PEET/files/_config.yaml.disable
new file mode 100644
index 0000000..64da532
--- /dev/null
+++ b/EM/PEET/files/_config.yaml.disable
@@ -0,0 +1,8 @@
+overlay: base
+relstage: stable
+group: EM
+shasums:
+  PEET/1.15.1a: de4e9104f90b9379502a34b58be33eafd5514d554002a94efe2adba6f44785e6
+
+PEET/1.15.1a:
+  - relstage: unstable
diff --git a/EM/PEET/files/variants b/EM/PEET/files/variants
new file mode 100644
index 0000000..202e7b9
--- /dev/null
+++ b/EM/PEET/files/variants
@@ -0,0 +1 @@
+PEET/1.15.1a	unstable	gcc/9.5.0 matlab/2020b
diff --git a/EM/PEET/modulefile b/EM/PEET/modulefile
new file mode 100644
index 0000000..7510133
--- /dev/null
+++ b/EM/PEET/modulefile
@@ -0,0 +1,30 @@
+#%Module1.0
+
+module-whatis           "PEET (Particle Estimation for Electron Tomography) is an open-source package for aligning and averaging particles in 3-D subvolumes extracted from tomograms."
+module-url              "https://bio3d.colorado.edu/PEET/"
+module-license	        "GPLv2 license"
+module-maintainer       "Spencer Bliven <spencer.bliven@psi.ch>"
+
+module-help	"
+PEET (Particle Estimation for Electron Tomography) is an open-source package
+for aligning and averaging particles in 3-D subvolumes extracted from
+tomograms. It seeks the optimal alignment of each particle against a
+reference volume through several iterations. If PEET and IMOD are both
+installed, most PEET operations are available from the eTomo graphical
+user interface in IMOD. PEET uses the parallel processing framework
+within IMOD, so that the lengthy computations can be distributed to
+multiple cores on one computer, to a set of linked workstations, or to
+a cluster. PEET is written in Matlab and a compiled version is
+distributed along with the Matlab runtime environment needed to run it. 
+
+> Nicastro D, Schwartz C, Pierson J, Gaudette R, Porter ME and McIntosh JR
+  (2006), \"The molecular architecture of axonemes revealed by cryoelectron
+  tomography.\", Science. Vol. 313(5789), pp. 944-948.
+  DOI:10.1126/science.1128618
+> Heumann JM, Hoenger A and Mastronarde DN (2011), \"Clustering and variance
+  maps for cryo-electron tomography using wedge-masked differences.\", J Struct
+  Biol. Vol. 175(3), pp. 288-299. DOI:10.1016/j.jsb.2011.05.011
+"
+
+setenv PARTICLE_DIR "$PREFIX"
+