neurodocker generates files with unprintable characters [when used with docker]

[satra]

@kaczmarj - we need to ensure that none of the generators contain non-printable characters.

+ '[' -n $'docker\r' -a -z '' ']'
+ '[' -x $'/usr/local/libexec/singularity/bootstrap-scripts/deffile-driver-docker\r.sh' ']'

on a unix system cat -v filename will show you the unprintable pieces. one can use dos2unix to remove them. otherwise, they go along even with copy and paste!

[kaczmarj]

@satra - i'm really sorry about all of the headaches that this bug caused. i can't see the unprintable characters on my debian machine with cat -v. the neurodocker command i tried is

neurodocker generate singularity \
  --base neurodebian:stretch \
  --pkg-manager apt \
  --install git emacs vim nano gedit

[satra]

@kaczmarj - try this:

docker run -it --rm kaczmarj/neurodocker:master generate singularity   \
 --base neurodebian:stretch-non-free   --pkg-manager apt   \
 --install eatmydata fsl-5.0-core fsl-mni152-templates  \
 --run "eatmydata apt-get -y install --no-install-recommends file"   \
 --add-to-entrypoint "source /etc/fsl/5.0/fsl.sh"

[kaczmarj]

@satra - yes, i can reproduce it now. thanks. building a new neurodocker image to see if that fixes the issue

[kaczmarj]

interestingly, running the neurodocker docker image produces the non-printable characters, but running a pip-installed neurdocker does not produce those characters (at least on my linux machine)

[satra]

ah - here you go:

moby/moby#8513 (comment)

[satra]

@kaczmarj - perhaps we can update the readme. no fix is needed.

[yarikoptic]

FWIW. oh, just ran into it myself, I should remember to not use -t with a docker run of neurodocker!!!