That's very helpful! One more question if you don't mind. In Lionel Henry's
solution, he changes ess-customize-alist to map inferior-ess-r-program to the
shell script that starts the container. If you have individual shell scripts in
each analysis directory, I assume you are not doing that? Or do I misunderstand
how ess-r-customize-alist works?
defun R-docker ()
(interactive)
(let ((ess-r-customize-alist
(append ess-r-customize-alist
'((inferior-ess-r-program . <shell script location goes
here>))))
(ess-R-readline t))
(R)))
Thanks so much,
Jim
-----Original Message-----
From: ESS-help <[email protected]> On Behalf Of Gavin Kelly via
ESS-help
Sent: Tuesday, November 19, 2024 5:57 AM
To: [email protected]
Subject: Re: [ESS] Emacs/ESS using Singularity container
I'm running ESS in similar HPC circumstances, and have adopted a similar
solution to the one in Lionel Henry's post. I tend to keep a shell script
along the lines of the following in every project, and it works 'fine'. It's
singularity, but I think apptainer is equivalent. Just in case it helps.
```
pwd=$(realpath ${PWD})
project_root=$(realpath $(git rev-parse --show-toplevel || echo ${pwd))
extra=--bind
$HOME/.Xauthority,$HOME/.Xdefaults,$HOME/.Xresources,$HOME/.emacs.d,$HOME/.ssh
--env DISPLAY=$DISPLAY # in real life, $extra is defined in elsewhere and is
only used in interactive sessions, not in e.g. makefiles.
cmd=R
image=bioconductor_docker_3.18-R-4.3.2.sif
singularity exec --bind ${project_root},/tmp --pwd ${pwd} --containall
--cleanenv --env
SQLITE_TMPDIR=/tmp,BIOCPARALLEL_WORKER_NUMBER=2,GITHUB_PAT=${GITHUB_PAT}
${extra} ${image} ${cmd} $@ ``` The Francis Crick Institute Limited is a
registered charity in England and Wales no. 1140062 and a company registered in
England and Wales no. 06885462, with its registered office at 1 Midland Road
London NW1 1AT
______________________________________________
[email protected] mailing list
https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/ess-help__;!!K-Hz7m0Vt54!kZsw4QAGEjvgcvGm2yIOYXWL9HXVCyZ_xygq22RiCXRtb6Q4IJz1MNikuNEZm29gn1PWPusW0iaf79DkTx1U5wmJIpk$
______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/ess-help
