update microscope lib settings

oist · Mar 27, 2024 · f87f94b · f87f94b
1 parent a0c48a4
commit f87f94b
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Showing 4 changed files with 12 additions and 1 deletion.
diff --git a/docs/gui/workflow.md b/docs/gui/workflow.md
@@ -229,7 +229,9 @@ You may not want to modify your original data folder, or you may want to make yo
 
      - get the C library files from the manufacturer's support.
      - use OptiNiSt by :ref:`developer mode <each-platforms-for-developer>`.
-     - put the libraries into ``optinist/studio/app/optinist/microscopes/dll/{nikon | olympus}/{linux | windows}/``
+     - set environment value ``MICROSCOPES_LIBRARY_DIR`` in ``studio/config/.env`` to your library path.
+     - put the libraries into ``MICROSCOPES_LIBRARY_DIR/dll/{nikon | olympus}/{linux | windows}/``
+     - If you use Linux, open ``studio/app/optinist/wrappers/optinist/conda/microscope.yaml`` and uncomment the ``- gcc=12`` line.
   ```
 
   <p align="center">

diff --git a/studio/app/dir_path.py b/studio/app/dir_path.py
@@ -1,6 +1,8 @@
 import os
 from enum import Enum
 
+from dotenv import load_dotenv
+
 _DEFAULT_DIR = "/tmp/studio"
 _ENV_DIR = os.environ.get("OPTINIST_DIR")
 
@@ -27,6 +29,7 @@ class DIRPATH:
     CONDAENV_DIR = (
         f"{os.path.dirname(os.path.dirname(os.path.dirname(__file__)))}/conda"
     )
+    load_dotenv(f"{CONFIG_DIR}/.env")
 
     SNAKEMAKE_FILEPATH = f"{APP_DIR}/Snakefile"
     EXPERIMENT_YML = "experiment.yaml"

diff --git a/studio/app/optinist/wrappers/optinist/conda/microscope.yaml b/studio/app/optinist/wrappers/optinist/conda/microscope.yaml
@@ -1,5 +1,8 @@
+channels:
+  - conda-forge
 dependencies:
   - python=3.9
+  # NOTE: Uncomment the following line if you want to use .nd2 .oir files on linux
   # - gcc=12
   - pip
   - pip:

diff --git a/studio/config/.env.example b/studio/config/.env.example
@@ -10,3 +10,6 @@ IS_STANDALONE=True
 # MYSQL_DATABASE=studio
 # MYSQL_USER=studio_db_user
 # MYSQL_PASSWORD=studio_db_password
+
+# NOTE: Uncomment and set your own values when using .nd2 or .oir reader
+# MICROSCOPES_LIBRARY_DIR="/app/studio/app/optinist/microscopes/dll"