From 51547afd7618b1cdf746c38d3fb08fe31d43deca Mon Sep 17 00:00:00 2001
From: Greta Assmann <greta.assmann@psi.ch>
Date: Mon, 16 Dec 2024 15:20:00 +0100
Subject: [PATCH] add topaz merlin7

---
 EM/topaz/README.md         | 34 ++++++++++++++++++++++++++++++++++
 EM/topaz/build             | 27 +++++++++++++++++++++++++++
 EM/topaz/environment.yaml  |  8 ++++++++
 EM/topaz/files/config.yaml | 13 +++++++++++++
 EM/topaz/modulefile        | 34 ++++++++++++++++++++++++++++++++++
 5 files changed, 116 insertions(+)
 create mode 100644 EM/topaz/README.md
 create mode 100755 EM/topaz/build
 create mode 100644 EM/topaz/environment.yaml
 create mode 100644 EM/topaz/files/config.yaml
 create mode 100644 EM/topaz/modulefile

diff --git a/EM/topaz/README.md b/EM/topaz/README.md
new file mode 100644
index 0000000..7b5063d
--- /dev/null
+++ b/EM/topaz/README.md
@@ -0,0 +1,34 @@
+# TOPAZ
+
+The topaz module is build for using it with the cryosparc software. An executable path to the topaz binary needs to be provided in cryosparc. 
+
+## Adding New Versions
+
+Adding new versions: change the environment file in the build folder accordingly (and the config.yaml file)  and run the build script.
+IMPORTANT: Build it on the GPU node , otherwise the pytorch installation will not enable GPU support. 
+
+## HINTS
+
+Current successful environment.yaml file: 
+
+channels:
+  - tbepler
+  - pytorch
+dependencies:
+  - python=3.6
+  - cudatoolkit
+  - topaz 
+  - pytorch
+
+- specifing cudatoolkit version of 11.8 failed for GPU support (see below)
+- specifing higher python/cudatoolkit versions lead to higher pytorch versions, which again failed for topaz to run successful (https://discuss.cryosparc.com/t/topaz-train-typeerror-concat-takes-1-positional-argument-but-2-were-given/11240/18) 
+
+## Versions
+
+Nov. 2024:  0.2.5 (TOPAZ) with 
+```
+python3.6
+cudatoolkit               11.3.1               h2bc3f7f_2  
+pytorch                   1.10.2          py3.6_cuda11.3_cudnn8.2.0_0
+pytorch-mutex             1.0                        cuda
+```
diff --git a/EM/topaz/build b/EM/topaz/build
new file mode 100755
index 0000000..789c7bd
--- /dev/null
+++ b/EM/topaz/build
@@ -0,0 +1,27 @@
+#!/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/topaz/environment.yaml b/EM/topaz/environment.yaml
new file mode 100644
index 0000000..8f19db7
--- /dev/null
+++ b/EM/topaz/environment.yaml
@@ -0,0 +1,8 @@
+channels:
+  - tbepler
+  - pytorch
+dependencies:
+  - python=3.6
+  - cudatoolkit
+  - topaz 
+  - pytorch
diff --git a/EM/topaz/files/config.yaml b/EM/topaz/files/config.yaml
new file mode 100644
index 0000000..6841a46
--- /dev/null
+++ b/EM/topaz/files/config.yaml
@@ -0,0 +1,13 @@
+---
+format: 1
+topaz:
+  defaults:
+    group: EM
+    overlay: base
+    relstage: unstable
+  versions:
+    0.2.5:
+      variants:
+        - overlay: Alps 
+          systems: [.*.merlin7.psi.ch]
+          relstage: unstable
diff --git a/EM/topaz/modulefile b/EM/topaz/modulefile
new file mode 100644
index 0000000..4527b50
--- /dev/null
+++ b/EM/topaz/modulefile
@@ -0,0 +1,34 @@
+#%Module
+
+module-whatis	        "A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph and tomogram denoising using deep denoising models."
+module-url		"https://github.com/tbepler/topaz"
+module-license	        "https://github.com/tbepler/topaz/blob/master/LICENSE"
+module-maintainer	"Greta Assmann  <greta.assmann@psi.ch>"
+
+module-help	"Particle Picker for CryoEM. Used with Cryosparc"
+
+# 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"
+    }
+}
+