From 51066a5431114e443298020a1640bdf88d86d083 Mon Sep 17 00:00:00 2001
From: Greta Assmann <greta.assmann@psi.ch>
Date: Thu, 19 Dec 2024 13:47:10 +0100
Subject: [PATCH] new DeepEMhancer merlin7

---
 EM/DeepEMhancer/build             | 34 +++++++++++++++++++++++++++++++
 EM/DeepEMhancer/environment.yaml  |  7 +++++++
 EM/DeepEMhancer/files/config.yaml | 13 ++++++++++++
 EM/DeepEMhancer/modulefile        | 34 +++++++++++++++++++++++++++++++
 4 files changed, 88 insertions(+)
 create mode 100755 EM/DeepEMhancer/build
 create mode 100644 EM/DeepEMhancer/environment.yaml
 create mode 100644 EM/DeepEMhancer/files/config.yaml
 create mode 100644 EM/DeepEMhancer/modulefile

diff --git a/EM/DeepEMhancer/build b/EM/DeepEMhancer/build
new file mode 100755
index 0000000..cbf5ff7
--- /dev/null
+++ b/EM/DeepEMhancer/build
@@ -0,0 +1,34 @@
+#!/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
+    "$PREFIX/miniconda/condabin/conda" env create --name "${P}_${V}" -f "$BUILDBLOCK_DIR/environment.yaml"
+        
+    
+    #activate env and download deep learning models 
+    mkdir -p "$PREFIX/deepmodels"
+    source "$PREFIX/miniconda/etc/profile.d/conda.sh" 
+    conda activate "${P}_${V}"
+    deepemhancer --download "$PREFIX/deepmodels"
+    conda deactivate
+} 
+
+#DO NOTHING
+pbuild::compile(){
+    :
+}
+
+pbuild::install(){
+    :
+}
+
+
+
+
diff --git a/EM/DeepEMhancer/environment.yaml b/EM/DeepEMhancer/environment.yaml
new file mode 100644
index 0000000..9a2d1d9
--- /dev/null
+++ b/EM/DeepEMhancer/environment.yaml
@@ -0,0 +1,7 @@
+channels:
+  - rsanchez1369
+  - anaconda
+  - conda-forge
+dependencies:
+  - python=3.10
+  - deepEMhancer
diff --git a/EM/DeepEMhancer/files/config.yaml b/EM/DeepEMhancer/files/config.yaml
new file mode 100644
index 0000000..5b4312b
--- /dev/null
+++ b/EM/DeepEMhancer/files/config.yaml
@@ -0,0 +1,13 @@
+---
+format: 1
+DeepEMhancer:
+  defaults:
+    group: EM
+    overlay: base
+    relstage: unstable
+  versions:
+    0.16:
+      variants:
+        - overlay: Alps 
+          systems: [.*.merlin7.psi.ch]
+          relstage: unstable
diff --git a/EM/DeepEMhancer/modulefile b/EM/DeepEMhancer/modulefile
new file mode 100644
index 0000000..657d101
--- /dev/null
+++ b/EM/DeepEMhancer/modulefile
@@ -0,0 +1,34 @@
+#%Module
+
+module-whatis	        "Deep cryo-EM Map Enhancer (DeepEMhancer) "
+module-url		"https://github.com/rsanchezgarc/deepEMhancer"
+module-license	        "Apache-2.0 License"
+module-maintainer	"Greta Assmann  <greta.assmann@psi.ch>"
+
+module-help	"DeepEMhancer is a python package designed to perform post-processing of cryo-EM maps as described in DeepEMhancer: a deep learning solution for cryo-EM volume post-processing, by Sanchez-Garcia et al, 2021."
+
+# Check for supported shell types
+set shelltype [module-info shelltype]
+switch -- $shelltype {
+    "sh" {
+        puts stdout "conda(){ :; };"
+        puts stdout "set +u"
+        puts stdout "source \"${PREFIX}\"/miniconda/etc/profile.d/conda.sh;\n"
+    }
+    default {
+        puts stderr "Shells of type '$shelltype' are NOT supported!"
+    }
+}
+
+
+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"
+    }
+}
+