From 6a28c61c089fcb50dc03d9836bc71c1c3f669f3e Mon Sep 17 00:00:00 2001
From: Greta Assmann <greta.assmann@psi.ch>
Date: Wed, 24 Jul 2024 11:51:17 +0200
Subject: [PATCH] add cryocare module

---
 EM/cryocare/README.md         | 11 +++++++++++
 EM/cryocare/build             | 23 +++++++++++++++++++++++
 EM/cryocare/environment.yaml  | 10 ++++++++++
 EM/cryocare/files/config.yaml |  8 ++++++++
 EM/cryocare/modulefile        | 34 ++++++++++++++++++++++++++++++++++
 5 files changed, 86 insertions(+)
 create mode 100644 EM/cryocare/README.md
 create mode 100755 EM/cryocare/build
 create mode 100644 EM/cryocare/environment.yaml
 create mode 100644 EM/cryocare/files/config.yaml
 create mode 100644 EM/cryocare/modulefile

diff --git a/EM/cryocare/README.md b/EM/cryocare/README.md
new file mode 100644
index 0000000..8570033
--- /dev/null
+++ b/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 
+
+
+
diff --git a/EM/cryocare/build b/EM/cryocare/build
new file mode 100755
index 0000000..d3169b1
--- /dev/null
+++ b/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(){
+    :
+}
diff --git a/EM/cryocare/environment.yaml b/EM/cryocare/environment.yaml
new file mode 100644
index 0000000..06b66c2
--- /dev/null
+++ b/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
diff --git a/EM/cryocare/files/config.yaml b/EM/cryocare/files/config.yaml
new file mode 100644
index 0000000..5efcd34
--- /dev/null
+++ b/EM/cryocare/files/config.yaml
@@ -0,0 +1,8 @@
+format: 1
+cryocare:
+  defaults:
+    group: EM
+    overlay: base
+    relstage: unstable
+  versions:
+    0.3.0:
diff --git a/EM/cryocare/modulefile b/EM/cryocare/modulefile
new file mode 100644
index 0000000..2c0f37a
--- /dev/null
+++ b/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"
+    }
+}
+
+