Tripal blast not run smoothly when using 'drush trp-run-jobs' command line about tripal_blast

[Naibin]

1 You can do this through the Drupal Admin UI by going to Administration > Configuration > Media > File System (admin/config/media/file-system). The Blast module is fully tested with alternative temporary directories. I check this setting page, looks nothing is wrong:

I also thought about changing the /tmp permissions to 777, but I still got the same error.

[root@localhost tmp]# chmod -R 777 ./

2 It is weird that it works when you click execute through the UI though. I wonder if you need to run tripal jobs on the command-line using the web user for your server?

yes, when I run command line, the -username=nd343 is a normal user. even though I use an admin user, the same error will return.

超级感谢您的指点！ Thank you very much for your advice!

@laceysanderson Finally, I changed the tmp folder to /var/www/tmp ， now that trpjob-daemon can be executed automatically. That's it, there is probably something wrong with the permissions of /tmp. In short, it is very good to be able to run the blast analysis function!

[laceysanderson]

Hi, this is definitely a permissions issue and is related to the configuration of your server not the blast module. Unfortunately I don't have any experience with private temp directories and thus have not come across this issue before nor do I have much guidance 😞

I would look at the drupal stackexchange or drupal.org for some guidance using keywords such as "File is not accessible temporary directory" and hopefully that will help 🤷‍♀️

Alternatively if this is a configuration of the server itself that you cannot change then a work around is to configure Drupal to use a different directory as the temporary directory. You can do this through the Drupal Admin UI by going to Administration > Configuration > Media > File System (admin/config/media/file-system). The Blast module is fully tested with alternative temporary directories.

It is weird that it works when you click execute through the UI though. I wonder if you need to run tripal jobs on the command-line using the web user for your server?

[Naibin]

1 You can do this through the Drupal Admin UI by going to Administration > Configuration > Media > File System (admin/config/media/file-system). The Blast module is fully tested with alternative temporary directories.
I check this setting page, looks nothing is wrong:

I also thought about changing the /tmp permissions to 777, but I still got the same error.

[root@localhost tmp]# chmod -R 777 ./

2 It is weird that it works when you click execute through the UI though. I wonder if you need to run tripal jobs on the command-line using the web user for your server?

yes, when I run command line, the -username=nd343 is a normal user.
even though I use an admin user, the same error will return.

超级感谢您的指点！ Thank you very much for your advice!

[laceysanderson]

Great! I am glad to hear you were able to get it working and my guidance helped!

One final clarification: when I said

I wonder if you need to run tripal jobs on the command-line using the web user for your server?

I was referring to the linux user that apache runs using (e.g. www-data on debian). I was wondering if you ran the drush command as that user... for example using su - to become that user before running the command... that then it would bypass your permission issue in the /tmp directory just as running through the UI does.