Merge branch '279-add-cryocare' into 'master'

Resolve "add cryocare"

Closes #279

See merge request Pmodules/buildblocks!443

EM/cryocare/README.md

@@ -0,0 +1,11 @@
+ Installation remarks for cryocare: 
+
+ - pip installation from https://pypi.org/project/cryoCARE/,   (see environment.yaml)
+ - creation of conda env with miniconda 
+
+Usage with Relion: module does not need to be activated , BUT : 
+- executables need to be provided in the relion GUI
+- the modulefile in RELION needs to add the cryocare bin to the LD_LIBRARY_PATH, otherwise the libraries will not be found 
+
+
+

EM/cryocare/build

@@ -0,0 +1,23 @@
+#!/usr/bin/env modbuild
+
+
+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::install(){
+    :
+}

EM/cryocare/environment.yaml

@@ -0,0 +1,10 @@
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.8
+  - cudatoolkit=11.0
+  - cudnn=8.0
+  - pip:
+    - tensorflow==2.4
+    - cryoCARE

EM/cryocare/files/config.yaml

@@ -0,0 +1,8 @@
+format: 1
+cryocare:
+  defaults:
+    group: EM
+    overlay: base
+    relstage: unstable
+  versions:
+    0.3.0:

EM/cryocare/modulefile

@@ -0,0 +1,34 @@
+#%Module1.0
+
+module-whatis           "Cryocare - Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data"
+module-url              "https://github.com/juglab/cryoCARE_T2T"
+module-license          "BSD 2-Clause Simplified License"
+module-maintainer       "Greta Assmann <greta.assmann@psi.ch>"
+
+module-help     "https://arxiv.org/abs/1810.05420"
+
+
+# Check for supported shell types
+set shelltype [module-info shelltype]
+switch -- $shelltype {
+    "sh" {
+        puts stdout "source \"${PREFIX}\"/miniconda/etc/profile.d/conda.sh;\n"
+    }
+    default {
+        puts stderr "Shells of type '$shelltype' are NOT supported!"
+    }
+}
+
+
+switch [module-info mode] {
+    "load" {
+      # Relies on the anaconda module being loaded since we need to update the path
+      puts stdout "conda activate ${P}_${V};\n"
+    }
+    "unload" -
+    "remove" {
+        puts stdout "conda deactivate;\n"
+    }
+}
+
+