Skip to content

Commit

Permalink
use -e flag to prevent supply of LC_ALL,LANG values
Browse files Browse the repository at this point in the history 
Fixes these warnings:
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
  LANGUAGE = (unset),
  LC_ALL = (unset),
  LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
Processing:..............................................Done
  • Loading branch information
@tashrifbillah
tashrifbillah committed Apr 3, 2024
1 parent 20792aa commit be770fb
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion workflows/_synb0_eddy.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ mkdir -p $TMPDIR
if [ ! -f OUTPUTS/b0_all_topup.nii.gz ]
then
TMPDIR=$TMPDIR \
singularity run -B INPUTS/:/INPUTS -B OUTPUTS/:/OUTPUTS \
singularity run -e -B INPUTS/:/INPUTS -B OUTPUTS/:/OUTPUTS \
-B ${NEW_SOFT_DIR}/fs7.1.0/license.txt:/extra/freesurfer/license.txt \
${NEW_SOFT_DIR}/containers/synb0-disco_v3.0.sif --stripped
fi
Expand Down

5 comments on commit be770fb

@tashrifbillah
Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

cc @RyanZurrin

@RyanZurrin
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Have you been able to verify that this indeed suppresses the unwanted terminal output warnings?

@tashrifbillah
Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

There is no reason to think I did not. It is an official code change.

@RyanZurrin
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Could you share the info you found about the -e flag? I was trying to find info on it, but I did not find much; that was the only reason I was asking.

@tashrifbillah
Copy link
Contributor Author

@tashrifbillah tashrifbillah commented on be770fb Apr 3, 2024 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

singularity shell --help

Please sign in to comment.