Merge pull request #48 from MELDProject/dev_docker

Dev docker
MELDProject · Sep 24, 2024 · 26f03a9 · 26f03a9
2 parents 06d3bd2 + 52028a3
commit 26f03a9
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diff --git a/docs/install_singularity.md b/docs/install_singularity.md
@@ -45,8 +45,9 @@ OR with Apptainer
 ```bash
 export APPTAINER_BINDPATH=/<path_to_meld_data_folder>:/data,<path_to_FS_license>/license.txt:/license.txt:ro
 export APPTAINERENV_FS_LICENSE=/license.txt
-3. Run this command to download the data folder 
+```
 
+3. Run this command to download the data folder 
 ```bash
 singularity exec meld_graph.sif /bin/bash -c "cd /app && python scripts/new_patient_pipeline/prepare_classifier.py "
 ```

diff --git a/scripts/env_setup.py b/scripts/env_setup.py
@@ -7,10 +7,8 @@ def setup():
         if sys.platform == "darwin":
             if os.path.exists("/Applications/freesurfer/7.2.0"):
                 os.environ["FREESURFER_HOME"] = "/Applications/freesurfer/7.2.0"
-
-    # check if FREESURFER_HOME is set up correctly
-    freesurfercheck = subprocess.run(['/bin/bash', '-c', "which freeview"], capture_output=True)
-    # Load freesurfer environment variables. This is equivalent to running the source command in a shell then running python, but for ease of use we set it up in process. 
+
+    freesurfercheck = subprocess.run(['/bin/bash', '-c', "type freeview"], capture_output=True)
     if freesurfercheck.returncode > 0:
         # A command that sources freesurfer
         source = 'source /Applications/freesurfer/7.2.0/SetUpFreeSurfer.sh'
@@ -25,7 +23,7 @@ def setup():
         if os.path.exists(f"{MELD_DATA_PATH}/license.txt"):
             print("setting license" + f"{MELD_DATA_PATH}/license.txt")
             os.environ["FS_LICENSE"] = f"{MELD_DATA_PATH}/license.txt"
-        elif os.path.exists(f"{os.getcwd()}/license.txt"):
+        if os.path.exists(f"{os.getcwd()}/license.txt"):
             print("setting license" + f"{os.getcwd()}/license.txt")
             os.environ["FS_LICENSE"] = f"{os.getcwd()}/license.txt"
         else: