Updated bind option for Singularity container.

- Allows creation of astropy cache in home directory if needed.
- Changed PermissionError to OSError

Author: cjproud

docker/Dockerfile

@@ -20,9 +20,5 @@ RUN pip install -r requirements.txt && \
     python setup.py install && \
     rm -rf /tmp/build
 
-
-WORKDIR /astropy/astropy
-
-ENV HOME=/tmp
-ENV XDG_CONFIG_HOME=/astropy
-ENV XDG_CACHE_HOME=/astropy
+#  set env
+ENV HOME=/tmp

nextflow.config

@@ -104,13 +104,13 @@ profiles {
     }
 }
 
-
 if ( host == "garrawarla") ) {
   // Set up container
   process.module = 'singularity/3.7.4'
   singularity {
     enabled = true
     envWhitelist = 'SINGULARITY_BINDPATH, SINGULARITYENV_LD_LIBRARY_PATH'
+    runOptions = '--bind $HOME:/$HOME'
   }
   params.containerDir = '/pawsey/mwa/singularity'
 

robbie.nf

@@ -156,7 +156,7 @@ process download_gleam_catalogue {
     try:
       cat.write(data_load.REF_CAT, format='fits')
       os.symlink(data_load.REF_CAT, "GLEAM_ref_cat.fits")
-    except PermissionError:
+    except OSError:
       # No permission so dump it here
       cat.write("GLEAM_ref_cat.fits", format='fits')
   """