1.9.9 for merlin7

EM/crYOLO/README.md

@@ -1,14 +1,15 @@
 # crYOLO
 
 crYOLO/1.2.3 was built as a miniconda independent environment.
-Subsequent versions are deployed as central conda environments.
-This significantly changed the build process.
+Subsequent versions (up to 1.6.1) are deployed as central conda environments
+
+crYOLO/1.9.9 (Merlin7, oct 2024) is  installed with an independent miniconda setup again. 
+
+From crYOLO/1.9.9 crYOLO exists as two different conda envs, one crYOLO (code itself) env, one napari (visualization) env. 
+The installation notes recommend to link one into another, on Merlin7 simply two different modules and envs exist.
+Users need to load one env in one terminal ( crYOLO itself) and another for visualization (napari).
 
 ## Adding New Versions
 
-To add a new version, first create the conda environment, as described in
-../../Programming/anaconda/2019.07/conda-env-defs/cryolo/.
-
-Next, update files/variants with the new version and run `./build <VERSION>` to
-install the modulefile
+Adding new versions: change the environment file in the build folder accordingly (and the config.yaml file)  and run the build script. 
 

EM/crYOLO/build

@@ -1,20 +1,27 @@
 #!/usr/bin/env modbuild
 
 
-pbuild::add_to_group 'EM'
-pbuild::prep() {
-    :
-}
-
 pbuild::configure() {
+    #MINICONDA INSTALL
+    mkdir -p  "$PREFIX/miniconda"
+    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O "$PREFIX/miniconda/miniconda.sh"
+    bash "$PREFIX/miniconda/miniconda.sh" -b -u -p "$PREFIX/miniconda/"
+
+ 
+    #CREATE ENV , make sure to source the "correct" conda.sh
+    "$PREFIX/miniconda/condabin/conda" env create --name "${P}_${V}" -f "$BUILDBLOCK_DIR/environment.yaml"
+
+}
+
+#DO NOTHING
+pbuild::compile(){
     :
 }
 
-pbuild::compile() {
+pbuild::install(){
     :
 }
 
-pbuild::install() {
-    :
-}
+
+
 

EM/crYOLO/files/config-1.2.3.sh

@@ -1,10 +0,0 @@
-# crYOLO configuration variables
-
-# Miniconda installer filename. Defaults to 'latest'
-MINICONDA_VERSION='Miniconda2-4.5.12-Linux-x86_64.sh'
-
-# cryoloBM download url
-CRYOLOBM_URL='ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_1_1/cryoloBM-1.1.1.tar.gz'
-# cryolo download url. Default:
-#CRYOLO_URL='ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_2_3/cryolo-1.2.3.tar.gz'
-

EM/crYOLO/files/config.yaml

@@ -0,0 +1,13 @@
+---
+format: 1
+crYOLO:
+  defaults:
+    group: EM
+    overlay: base
+    relstage: unstable
+  versions:
+    1.9.9:
+      variants:
+        - overlay: Alps 
+          systems: [.*.merlin7.psi.ch]
+          relstage: unstable

EM/crYOLO/files/variants

@@ -1,5 +0,0 @@
-crYOLO/1.2.3	deprecated	cuda/9.0.176
-crYOLO/1.5.6_gpu	stable	anaconda/2019.07
-crYOLO/1.6.1_gpu	stable	anaconda/2019.07
-crYOLO/1.6.1_cpu	stable	anaconda/2019.07
-

EM/crYOLO/modulefile

@@ -3,7 +3,7 @@
 module-whatis	        "crYOLO is a fast and accurate particle picking procedure for electron microscopy"
 module-url		"http://sphire.mpg.de/wiki/doku.php?id=pipeline:window:cryolo"
 module-license	        "SPHIRE-crYOLO Complimentary Science Software License (http://sphire.mpg.de/wiki/doku.php?id=cryolo_license). Non-commercial academic and research purposes only"
-module-maintainer	"Spencer Bliven <spencer.bliven@psi.ch>"
+module-maintainer	"Greta Assmann  <greta.assmann@psi.ch>"
 
 module-help	"
 CrYOLO is a fast and accurate particle picking procedure. It's based on
@@ -26,28 +26,20 @@ convolutional neural networks and utilizes the popular You Only Look Once
 set shelltype [module-info shelltype]
 switch -- $shelltype {
     "sh" {
-        puts stdout "source \"\${ANACONDA_PREFIX}\"/admintools/conda_setup.sh;\n"
+        puts stdout "conda(){ :; };"
+        puts stdout "set +u"
+        puts stdout "source \"${PREFIX}\"/miniconda/etc/profile.d/conda.sh;\n"
     }
     default {
         puts stderr "Shells of type '$shelltype' are NOT supported!"
     }
 }
 
-# Determine useflags and construct conda env name
-set list [split $V "_"]
-set version  [lindex ${list} 0]
-set useflags [lrange ${list} 1 end]
-set flavour  [lindex $useflags 0]
-set env_to_activate [string tolower ${P}]-${version}-${flavour}
-
-#puts stderr "P/V: $P/$V"
-#puts stderr "USEFLAG: [lindex $useflags 0]"
-#puts stderr "$env_to_activate"
 
 switch [module-info mode] {
     "load" {
       # Relies on the anaconda module being loaded since we need to update the path
-      puts stdout "conda activate $env_to_activate;\n"
+      puts stdout "conda activate ${P}_${V};\n"
     }
     "unload" -
     "remove" {