Merge pull request #8 from DCAN-Labs/hotfix/singularity

hotfix for singularity containers

README.md

@@ -55,13 +55,16 @@ docker run --rm \
 To call using Singularity:
 
 ```{bash}
-singularity run \
+env -i singularity run \
     -B /path/to/bids_dataset:/bids_input \
     -B /path/to/outputs:/output \
-    -B /path/to/freesurfer/license:/license \
-    ./abcd-hcp-pipeline.img /bids_input /output --freesurfer-license=/license [OPTIONS]
+    -B /path/to/freesurfer/license.txt:/opt/freesurfer/license.txt \
+    ./abcd-hcp-pipeline.img /bids_input /output --freesurfer-license=/opt/freesurfer/license.txt [OPTIONS]
 ```
 
+notice that the license is now mounted directly into the freesurfer folder, 
+and the call to singularity is prefaced by "env -i"
+
 ### Options:
 
 ```{bash}

app/helpers.py

@@ -278,6 +278,8 @@ def validate_license(freesurfer_license):
         assert os.path.exists(license_txt), \
             'freesurfer license.txt not located. You can provide a license ' \
             'file using the --freesurfer-license <LICENSE> argument.'
+    elif os.path.normpath(license_txt) == os.path.normpath(freesurfer_license):
+        pass
     else:
         import shutil
         shutil.copy(freesurfer_license, license_txt)