bash: /usr/local/bin/nextflow: Permission denied

[GKerdivel]

Bug report

A colleague installed nextflow on our server following the documentation provided in this github (using curl). He gave execution right to all but yet only him can launch it using nextflow run scrip.nf. All other users have to launch sudo nextflow run scrip.nf or get the message

bash: /usr/local/bin/nextflow: Permission denied

Expected behavior and actual behavior

Expected behavior : All users should be able to launch nextflow without superuser rights
Actual behavior : Apart from the one user who installed nextflow on the server, all other users have to be sudoers to launch nextflow

Steps to reproduce the problem

NA

Program output

bash: /usr/local/bin/nextflow: Permission denied

Environment

• Nextflow version: 21.10.6
• Java version: opendjdk 11.0.15
• Operating system: Ubuntu 20.04.4 LTS
• Bash version: 5.0.17

Additional context

I tried to change the rights (chmod 777), changing the owner to and/or group to root or to change the group to a group common to all users. I also tried to change the localization of the nextflow file. None of that changed anything.

[mribeirodantas]

Can you run the command below and share the output here, please?

stat `whereis nextflow`

This command will give us information about the Nextflow binary, such as permissions, file owner and file owner group. Maybe that will help us understand what's going on.

[lholivera]

Same problem. This permissions: Access: (0711/-rwx--x--x) Uid: ( 1003/leonidax) Gid: ( 1003/leonidax)

[mgurbano]

Same problem. My permissions are slightly different than the comment above: Access: (0777/lrwxrwxrwx) Uid: (0/root) Gid: (0/root). I have 777 access... So I'm very unsure as to why my permission is denied.

[mribeirodantas]

Can you please confirm that you have permission for the whole path? If you have permission to execute a file but do not have permission to access the path where the file is located, you'll get permission denied. See the example below:

➜  ~ a/b/example.sh
oi
➜  ~ chmod 000 a
➜  ~ a/b/example.sh
zsh: permission denied: a/b/example.sh

[rusalkaguy]

I get this problem when trying to run a docker container (which uses nextflow internally) using singularity (thus, no root), because I'm on a shared cluster.

singularity exec docker://bioraddbg/sequoia_analysis_toolkit /bin/bash /opt/biorad/src/entrypoint.sh --help
gives
/bin/bash: /usr/local/bin/nextflow: Permission denied

while
singularity exec docker://bioraddbg/sequoia_analysis_toolkit ls -lsd /usr/ /usr/local /usr/local/bin /usr/local/bin/nextflow
shows path is accessible and nextflow should be executable.
0 drwxr-xr-x 10 root root 162 Oct 10 2019 /usr/
0 drwxr-xr-x 10 root root 135 Oct 10 2019 /usr/local
0 drwxr-xr-x 2 root root 112 Oct 22 2020 /usr/local/bin
16 -rwx--x--x 1 root root 15478 Oct 22 2020 /usr/local/bin/nextflow

[gelio5]

Get this problem too.
Error was in reading permission.
Solved by sudo chmod 715 /usr/local/bin/nextflow

[bounlu]

I have this issue every time I upgrade Nextflow with sudo nextflow self-update. The permission of the executable file /usr/local/bin/nextflow becomes 644, and I have to manually change it to 755. I believe 755 must be the default. Is there any reason why not so?

[pditommaso]

Nextflow cannot change the file permission because it would require sudo

[bounlu]

Yes I use sudo to upgrade nextflow for all the users and it reverts back the permissions.