planemo serve breaks with new docker version when running tools

[pcm32]

I recently updated docker to Docker version 24.0.6, build ed223bc, but now when running planemo with --biocontainers, tools fail to run with an error 125 showing:

docker: invalid spec: ::rw: empty section between colons.
See 'docker run --help'.

Has anyone encountered this?

I also see in the logs:

galaxy.tool_util.output_checker INFO 2023-10-03 18:27:40,635 [pN:main.1,p:85022,tN:LocalRunner.work_thread-0] Job error detected, failing job. Reasons are [{'type': 'exit_code', 'desc': 'Fatal error: Exit code 125 ()', 'exit_code': 125, 'code_desc': '', 'error_level': 3}]

Thanks!

[pcm32]

Tried the planemo setup I previously had and the current version, same result.

[pcm32]

Seems to be related to some env vars not being set and docker no longer ignoring these empty -v ::rw:

bash /private/var/folders/cs/zzjgpzj142934pd0j29gnk_r0000gq/T/tmpnz_qw7h8/job_working_directory/000/29/galaxy_29.sh
TMP:
TMPDIR: /var/folders/cs/zzjgpzj142934pd0j29gnk_r0000gq/T/
TEMP:
_GALAXY_JOB_TMP_DIR: /private/var/folders/cs/zzjgpzj142934pd0j29gnk_r0000gq/T/tmpnz_qw7h8/job_working_directory/000/29/tmp

and the the command having:

-v "$_GALAXY_JOB_TMP_DIR:$_GALAXY_JOB_TMP_DIR:rw" -v "$TMPDIR:$TMPDIR:rw" -v "$TMP:$TMP:rw" -v "$TEMP:$TEMP:rw"

so some of those end empty.

[mvdbeek]

That should be an old version of 23.1 and should have been fixed since. Can you confirm that this is the problem ?

[pcm32]

Could be, will check the underlying galaxy version used and retry with a newer one if too old.

[pcm32]

...mmm... I just retried with the 23.1 from the release 23.1 branch, I haven't double checked that is the same env var problems, but I'm getting err 125 from docker (it doesn't show the same message as before though).