Galaxy newbie here. I have a brand new v20.01 instance but am having a problem getting user PAM based user logins to work correctly.
The problem it seems to me has to do with the service not having sufficient permissions to create a 'new' user account folder because it wants to append our org's email suffix to the folder name instead of just detecting that the correctly named username folder without the suffix in fact already exists (mounted via NFS), and therefore does not need to be created.
Note that this mechanism was previously working in v19.05.
Here is the issue:
galaxy.webapps.galaxy.controllers.user DEBUG 2020-04-30 16:25:49,481 [p:86293,w:1,m:0] [uWSGIWorker1Core0] trans.app.config.auth_config_file: /hpc/software/installed/galaxy/20.01/config/auth_conf.xml
galaxy.auth.providers.pam_auth DEBUG 2020-04-30 16:25:49,482 [p:86293,w:1,m:0] [uWSGIWorker1Core0] use username: True use email False email None username sandra
galaxy.auth.providers.pam_auth DEBUG 2020-04-30 16:25:49,482 [p:86293,w:1,m:0] [uWSGIWorker1Core0] PAM auth: will use external helper: False
galaxy.auth.providers.pam_auth DEBUG 2020-04-30 16:25:49,868 [p:86293,w:1,m:0] [uWSGIWorker1Core0] PAM authentication successful for sandra
galaxy.auth.util DEBUG 2020-04-30 16:25:49,873 [p:86293,w:1,m:0] [uWSGIWorker1Core0] Email: sandra(a)mcri.edu.au, auto-register with username: sandra
galaxy.web.framework.decorators ERROR 2020-04-30 16:25:50,042 [p:86293,w:1,m:0] [uWSGIWorker1Core0] Uncaught exception in exposed API method:
Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 282, in decorator
rval = func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/controllers/user.py", line 122, in login
return self.__validate_login(trans, payload, **kwd)
File "lib/galaxy/webapps/galaxy/controllers/user.py", line 147, in __validate_login
message, user = self.__autoregistration(trans, login, password)
File "lib/galaxy/webapps/galaxy/controllers/user.py", line 105, in __autoregistration
File "lib/galaxy/web/framework/webapp.py", line 720, in handle_user_login
File "lib/galaxy/web/framework/webapp.py", line 665, in user_checks
File "lib/galaxy/web/framework/webapp.py", line 657, in check_user_library_import_dir
File "lib/galaxy/util/path/__init__.py", line 114, in safe_makedirs
File "/hpc/software/installed/galaxy/20.01/.venv/lib64/python3.6/os.py", line 220, in makedirs
PermissionError: [Errno 13] Permission denied: '/home/sandra(a)mcri.edu.au'
Here is the auth_conf.xml:
FYI in case it's relevant the server's sssd.conf has also been customised to drop the domain suffix.
Any ideas? Is there perhaps some additional config in the v20.01 galaxy.yml that I've missed?
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I submitted 2 bed files for upload to Galaxy a couple of hours ago, and it shows "the job is waiting to run." I have never had an upload take so long. The status page said everything was working normally with no issues reported today.
Is there an issue with the job queue or is the system just heavily loaded?
I am i the process to deploy a local instance of the galaxy server and all seems to work pretty ok.
There is only one issue, so far, that is really puzzling me and that is "checkboxes". Can't seem to find a way to tick them!
For example, I am trying to get the blast+ tool but there is no way I can get those options "visukaly" set. I can see that the flag is correctly raised when clicking the option, but the user cants see what was selected or not.
Anyone had the same experience? Anyone has a solution to this?
Here is a snippet of the code I could fish out.
<div class="ui-option" data-original-title="" title="">
<input id="uid-767" type="radio" name="field-uid-765" value="blastp">
<label class="ui-options-label" for="uid-767">::before
blastp - Traditional BLASTP to compare a protein query to a protein database</label></div>
<div class="ui-option" data-original-title="" title="">
<input id="uid-768" type="radio" name="field-uid-765" value="blastp-fast">
<label class="ui-options-label" for="uid-768">::before
blastp-fast - Use longer words for seeding, faster but less accurate</label></div>
<div class="ui-option" data-original-title="" title=""><input id="uid-769" type="radio" name="field-uid-765" value="blastp-short">
<label class="ui-options-label" for="uid-769">::before
blastp-short - BLASTP optimized for queries shorter than 30 residues</label>
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