new version 5.0.0 on merlin7

EM/IMOD/README.md

@@ -12,3 +12,7 @@ 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).
+
+TODO solution: re-write the .sh script that is sourced in the modulefile into the 
+modulefile directly. Variables and Path extensions will then automatically be 
+"unset" when unloding. 

EM/IMOD/build

@@ -1,18 +1,16 @@
 #!/usr/bin/env modbuild
-set -e
 
-pbuild::add_to_group 'EM'
 
 
 pbuild::prep() {
     : ${CUDA_VERSION:?No CUDA_VERSION set}
+    #local cuda="${CUDA_VERSION%.*}"  IF the cua version matches the cuda version in the filename 
     local cuda="${CUDA_VERSION%.*}"
-    local filename="imod_${V_PKG}_RHEL7-64_CUDA${cuda}.sh"
+    #otherwise: 
-    if [[ $V_RELEASE == *beta* ]]; then
+    local cuda="12.0"
-        local url="https://bio3d.colorado.edu/ftp/latestIMOD/RHEL7-64_CUDA${cuda}/$filename"
+    local filename="imod_${V_PKG}_RHEL8-64_CUDA${cuda}.sh"
-    else
+    # beta release link for Merlin7 ( RH8 for Opensuse)
-        local url="https://bio3d.colorado.edu/imod/AMD64-RHEL5/$filename"
+    local url="https://bio3d.colorado.edu/ftp/latestIMOD/RHEL8-64_CUDA${cuda}/$filename"
-    fi
     local dst="$PMODULES_DISTFILESDIR/${filename}"
     if [ -f "$dst" ]; then
         echo "Found cached $dst" >&2
@@ -35,8 +33,11 @@ pbuild::compile() {
 
 pbuild::install() {
     : ${CUDA_VERSION:?No CUDA_VERSION set}
-    local cuda="${CUDA_VERSION%.*}"
+    #local cuda="${CUDA_VERSION%.*}"
-    local filename="imod_${V_PKG}_RHEL7-64_CUDA${cuda}.sh"
+    #(if cuda version matches the file name) if not:
+    local cuda="12.0"
+    
+    local filename="imod_${V_PKG}_RHEL8-64_CUDA${cuda}.sh"
     local dst="$PMODULES_DISTFILESDIR/${filename}"
 
     mkdir -p "$PREFIX/profile.d"

EM/IMOD/files/config.yaml

@@ -0,0 +1,15 @@
+---
+format: 1
+IMOD:
+  defaults:
+    group: EM
+    overlay: base
+    relstage: unstable
+  versions:
+    5.0.0:
+      variants:
+        - overlay: Alps 
+          systems: [.*.merlin7.psi.ch]
+          relstage: unstable
+          runtime_deps:
+            - cuda/12.2.0 

EM/IMOD/files/variants

@@ -1,4 +0,0 @@
-IMOD/4.9.5	stable	
-IMOD/4.11.20	stable	cuda/10.1.105
-IMOD/4.11.24	unstable	cuda/10.1.105
-IMOD/4.12.50-beta	unstable	cuda/10.1.105

EM/IMOD/modulefile

@@ -3,7 +3,7 @@
 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-maintainer        "Greta Assmann - greta.assmann@psi.ch" 
 
 module-help        "
 IMOD is a set of image processing, modeling and display programs used for tomographic
@@ -34,6 +34,11 @@ For tomographic reconstruction, see also:
 > tomographic reconstruction in IMOD. J. Struct. Biol. 197:102-113. 
 "
 
+# TO DO : rewrite IMOD-linx.sh script directly into the following section instead of sourcing the script
+
+#this is needed to NOT set the default IMOD_DIR by pmodules, as this is set later in the IMOD-linux.sh
+set dont-setenv { IMOD_DIR }
+
 switch [module-info mode] {
     "load" {
         puts stdout "source $PREFIX/profile.d/IMOD-linux.sh"