Mnt/create wrappers var

share/fsl/sbin/update_fsl_package

@@ -94,7 +94,8 @@ def conda(cmd : str, capture_output=True, **kwargs) -> str:
 
     # If FSLDIR is a child env, we won't be able
     # to find the conda executable. In this case,
-    # we have to assume  that we can call "conda".
+    # we have to assume that "conda" is on the
+    # $PATH, or is defined as a shell function.
     candidates = [
         op.join(fsldir, 'bin',      'conda'),
         op.join(fsldir, 'condabin', 'conda'),
@@ -544,11 +545,19 @@ def install_packages(packages : Sequence[Package], dry_run : bool):
     packages = [f'"{p.name}={p.version}"' for p in packages]
     cmd      = f'install --no-deps -p {fsldir} -y ' + ' '.join(packages)
 
+    # We need to set this variable to ensure that
+    # FSL command wrapper scripts are created in
+    # $FSLDIR/share/fsl/bin/. See
+    # $FSLDIR/share/fsl/sbin/createFSLWrapper for
+    # more details.
+    env = os.environ.copy()
+    env['FSL_CREATE_WRAPPER_SCRIPTS'] = 1
+
     print('\nInstalling packages...')
     if dry_run:
         print(f'Dry run - would execute {cmd}')
     else:
-        conda(cmd, False)
+        conda(cmd, False, env=env)
 
 
 def parse_args(argv : Optional[Sequence[str]]) -> argparse.Namespace: