Merge branch 'dynamo' into 'master'

Initial dynamo/1.1.514 buildblock

See merge request Pmodules/buildblocks!157

EM/dynamo/1.1.514/config

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+# Google drive file hash, from https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Downloads
+DYNAMO_ID=1gZA97VTDVOTurtwX7Nw7F3VcEvfWcm3J
+

EM/dynamo/README.md

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+# Dynamo
+
+## Installation
+
+Installation was only partially automated in the build script. Currently only the 'prep' step is implemented. Future versions will add more commands to the build script.
+
+Installation should be done on merlin with an -adm account
+
+1. Add new version to `files/variants`
+2. Add google drive download link to `$V/config`.
+3. Run `build <version>`
+4. module load dynamo/$V
+5. Compile stand-alone: `dynamo_setup_linux.sh`
+6. Compile MPI: `source dynamo_setup_cluster.sh mpic++ dynamo_activate_linux_shipped_MCR.sh`
+7. Compile Cuda:
+
+    cd $DYNAMO_ROOT/cuda
+    make clean
+    ./config.sh
+    grep CUDA_ROOT makefile
+    make all
+    make extended
+
+

EM/dynamo/build

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+#!/usr/bin/env modbuild
+
+pbuild::add_to_group 'EM'
+pbuild::use_cmake
+
+# config provides DYNAMO_ID
+test -f "$V/config" || { echo "$V/config not found"; exit 1; }
+source "$V/config"
+
+
+pbuild::prep() {
+    # Download tarball and expand to $PREFIX
+    # Download links are on google drive, which requires a script (gdrivedl.py)
+    # to handle setting session cookies
+
+    local GDRIVEDL="${PMODULES_TMPDIR:-/tmp}/gdrivedl.py"
+
+    bootstrap () {
+        # Download gdrivedl to bootstrap the download process
+        if ! [ -f "$GDRIVEDL" ]; then
+            # Use sbliven fork; adds CLI options
+            wget -O "$GDRIVEDL" 'https://raw.githubusercontent.com/sbliven/gdrivedl/master/gdrivedl.py'
+        fi
+    }
+
+    download_dynamo() {
+        local DYNAMO_ID="$1"
+        #local DYNAMO_LINK="https://drive.google.com/u/0/uc?export=download&id=${DYNAMO_ID}"
+        local OUT="$2"
+
+        bootstrap
+
+        python "$GDRIVEDL" "$DYNAMO_ID" -O "$OUT" --quiet
+    }
+
+    unpack() {
+        local -r file="$1"
+        local -r dir="${2:-${SRC_DIR}}"
+        (
+            if [[ -n "${dir}" ]]; then
+                mkdir -p "${dir}"
+                cd "${dir}"
+            fi
+            tar -xv --strip-components 1 -f "${file}"
+        )
+    }
+
+    : DYNAMO_ID=${DYNAMO_ID:?DYNAMO_ID not set in config file}
+    TAR_FILE="$PMODULES_DISTFILESDIR/dynamo-${V_PKG}.tar"
+    mkdir -p "${PMODULES_DISTFILESDIR}"
+    download_dynamo "$DYNAMO_ID" "$TAR_FILE"
+    mkdir -p "$PREFIX"
+    unpack "$TAR_FILE" "$PREFIX/bin"
+}
+
+pbuild::configure() {
+    :
+}
+
+pbuild::compile() {
+    # Could force compilation here, but I'm going to do it manually the first time
+    :
+}
+
+pbuild::install() {
+    :
+}
+

EM/dynamo/files/variants

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+dynamo/1.1.514	unstable	b:psi-python36/5.0.1 gcc/9.3.0 openmpi/4.0.4_slurm cuda/11.1.0 matlab/2019a

EM/dynamo/modulefile

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+#%Module1.0
+
+module-whatis           "a software environment for subtomogram averaging of cryo-EM data"
+module-url              "https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Main_Page"
+module-license          "GPLv2 license"
+module-maintainer       "Spencer Bliven <spencer.bliven@psi.ch>"
+
+module-help             "
+Dynamo is a software environment for subtomogram averaging of cryo-EM data.  In
+a full workflow, you would organize tomograms in catalogues, use them to pick
+particles and create alignment and classification projects to be run on
+different computing environments. 
+
+Cite:
+
+1. Dynamo: A flexible, user-friendly development tool for subtomogram averaging
+   of cryo-EM data in high-performance computing environments. Castaño-Díez D,
+   Kudryashev M, Arheit M, Stahlberg H., J Struct Biol. 2012.
+2. Dynamo Catalogue: Geometrical tools and data management for particle picking
+   in subtomogram averaging of cryo-electron tomograms Castaño-Díez D, Kudryashev
+   M, Stahlberg H., in J Struct Biol. 2017 Feb; 197(2):135-144
+3. The Dynamo package for tomography and subtomogram averaging: components for
+   MATLAB, GPU computing and EC2 Amazon Web Services Castaño-Díez D. in Acta
+   Crystallographica Section D: Structural Biology 73 (6).
+4. Protocols for Subtomogram Averaging of Membrane Proteins in the Dynamo
+   Software Package Navarro PP, Stahlberg H and Castaño-Díez D (2018). Front. Mol.
+   Biosci. 5:82.
+"
+
+setenv DYNAMO_ROOT "$PREFIX/bin"
+# merlin-specific
+setenv MCR_CACHE_ROOT "/scratch/$::env(USER)"