Merge branch '307-peet_1-17-0_merlin7' into 'master'

Resolve "PEET_1.17.0_merlin7"

Closes #307

See merge request Pmodules/buildblocks!474

EM/PEET/README.md

@@ -6,9 +6,7 @@
 
 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.
+This module is usually used in combination with IMOD (etomo GUI). 
 
 ## Testing
 
@@ -16,12 +14,17 @@ This should probably not be used until yaml support in modbuild stabilizes.
 
 ## 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.
+pbuild::install update this file so that it reads the loaded modules correctly. 
+(Remark Nov. 2024: still true for version 1.17.0) 
 
+## Versions
+
+According to the website (INSTALL.TXT) the following Matlab is needed : 
+
+-1.17.0 : 2022b  (Merlin7, automatically loads matlab)

EM/PEET/build

@@ -1,6 +1,5 @@
 #!/usr/bin/env modbuild
 
-pbuild::add_to_group 'EM'
 
 
 pbuild::prep() {
@@ -13,6 +12,7 @@ pbuild::prep() {
             --fail \
             --output "$dst" \
             "https://bio3d.colorado.edu/ftp/PEET/linux/Particle_${V_PKG}_linux.sh"
+            --no-check-certificate
     fi
     }
 

EM/PEET/files/_config.yaml.disable

@@ -1,8 +0,0 @@
-overlay: base
-relstage: stable
-group: EM
-shasums:
-  PEET/1.15.1a: de4e9104f90b9379502a34b58be33eafd5514d554002a94efe2adba6f44785e6
-
-PEET/1.15.1a:
-  - relstage: unstable

EM/PEET/files/config.yaml

@@ -0,0 +1,16 @@
+---
+format: 1
+PEET:
+  defaults:
+    group: EM
+    overlay: base
+    relstage: unstable
+  versions:
+    1.17.0:
+      variants:
+        - overlay: Alps 
+          systems: [.*.merlin7.psi.ch]
+          relstage: unstable
+          runtime_deps:
+            - gcc/12.3.0
+            - matlab/2022b

EM/PEET/files/variants

@@ -1,2 +0,0 @@
-PEET/1.15.1a	stable	gcc/9.5.0 matlab/2020b
-PEET/1.16.0	stable	gcc/9.5.0 matlab/2021b

EM/PEET/modulefile

@@ -3,7 +3,7 @@
 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-maintainer       "Greta Assmann <greta.assmann@psi.ch>"
 
 module-help	"
 PEET (Particle Estimation for Electron Tomography) is an open-source package