[Neurodebian-devel] Problem with fsl_app_wrapper

[Michael Hanke]

Hi,

On Wed, Sep 19, 2012 at 05:31:20PM -0700, Brendan Moloney wrote:
> I was quite excited to see the new FSL 5.0 release and started to plan
> our migration. During the transition period I would like the default
> commands (e.g. 'flirt') to use 4.1 and allow users to explicitly
> request the updated versions (e.g. by running 'fsl5.0-flirt'). To
> achieve this I made '/etc/fsl/fsl.sh' point to '/etc/fsl/4.1/fsl.sh'
> (our default bash.bashrc then calls '/etc/fsl/fsl.sh' to set up the
> environment).
> 
> This does not work because fsl_app_wrapper only sets up the correct
> environment if FSLDIR is not already defined. So calling
> 'fsl5.0-flirt' still runs the flirt command from 4.1.

Thanks for your report. This seems like a very suboptimal behavior. I'd
propose to apply this patch:

diff --git a/debian/fsl_app_wrapper b/debian/fsl_app_wrapper
index 6f7f37b..5a1af30 100644
--- a/debian/fsl_app_wrapper
+++ b/debian/fsl_app_wrapper
@@ -20,11 +20,10 @@ if [ "${cmd}" = "fsl_app_wrapper" ]; then
     exit 1
 fi
 
-# Set up the FSL paths if necessary (if the user hasn't overriden them
-
-if [ -z "${FSLDIR}" ]; then
-    . /etc/fsl/5.0/fsl.sh
-fi
+# Set up the FSL paths if necessary
+# do not allows user-override, as this wrapper is used via
+# versioned symlinks
+. /etc/fsl/5.0/fsl.sh
 
 abs_cmd=${FSLDIR}/bin/${cmd}
 if [ ! -x $abs_cmd ]; then


If you do not object, I'd go ahead and change the next release to use
this patch.

Thanks again,

Michael

-- 
Michael Hanke
http://mih.voxindeserto.de