hexylena
commented
2 years ago Looks like the tmpdir is set to a read only filesystem, I'm not sure why that's happened.
Open mblue9 opened 2 years ago
hexylena
commented
2 years ago Looks like the tmpdir is set to a read only filesystem, I'm not sure why that's happened.
hexylena
commented
2 years ago This is an issue with the UseGalaxy.eu deployment it seems. @bgruening @gmauro can help further I imagine. The temp directories are set to the job_working_directory's working dir which makes some sense
$ env | grep job_working | sort
CWD=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/working/rstudio
_GALAXY_JOB_HOME_DIR=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/home
_GALAXY_JOB_TMP_DIR=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/tmp
GALAXY_WORKING_DIR=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/working
PWD=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/tmp
TEMP=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/tmp
TMP=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/tmp
TMPDIR=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/tmpBut I'm not quite sure why that's read only. Additionally I'm not sure it makes sense to put tmp on a networked filesystem, rather than /tmp/ within the container? But maybe they can provide additional context here.
Or maybe just a mixup because the server runs as the user within the container (rstudio) and the directories have been set to rstudio-servers's permissions
(base) rstudio@ce164b22683a:/data/dnb03/galaxy_db/job_working_directory/034/747/34747228$ whoami
rstudio
(base) rstudio@ce164b22683a:/data/dnb03/galaxy_db/job_working_directory/034/747/34747228$ ls -al working _working home
home:
total 45
drwxr-xr-x. 2 rstudio-server rstudio-server 0 Nov 22 11:17 .
drwxr-xr-x. 11 rstudio-server rstudio-server 922 Nov 22 11:17 ..
_working:
total 45
drwxr-xr-x. 2 rstudio-server rstudio-server 0 Nov 22 11:17 .
drwxr-xr-x. 11 rstudio-server rstudio-server 922 Nov 22 11:17 ..
working:
total 48
drwxr-xr-x. 3 rstudio-server rstudio-server 25 Nov 22 11:17 .
drwxr-xr-x. 11 rstudio-server rstudio-server 922 Nov 22 11:17 ..
drwxr-xr-x. 4 root root 47 Nov 22 11:17 rstudio
mblue9
commented
2 years ago Ok, thanks for investigating and the info @hexylena !
hexylena
commented
2 years ago You can probably "export TMP=/tmp" (and again for the other variant spellings that were set in what I pasted) in the short term to work around it!
On Mon, Nov 22, 2021, 16:47 mblue9 @.***> wrote:
Ok, thanks for investigating and the info @hexylena https://github.com/hexylena !
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/hexylena/docker-rstudio-notebook/issues/37#issuecomment-975660089, or unsubscribe https://github.com/notifications/unsubscribe-auth/AADP7O6BCMA6T5YAQPLP3Q3UNJQZHANCNFSM5IMCDP6Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
hexylena
commented
2 years ago still seems to be an issue @bgruening, is there a way EU can change the permissions of the JWD tmp dir such that RStudio can write to it?
Hello,
Was trying out installing an R package in Galaxy EU RStudio terminal, following the instructions in the RStudio console
mamba install package, but it didn't work with mamba (conda seems to work, or at least get further). Should I be able to install using mamba?