pam login issue
by Sandra Maksimovic
Hi there,
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
trans.handle_user_login(user)
File "lib/galaxy/web/framework/webapp.py", line 720, in handle_user_login
self.user_checks(user)
File "lib/galaxy/web/framework/webapp.py", line 665, in user_checks
self.check_user_library_import_dir(user)
File "lib/galaxy/web/framework/webapp.py", line 657, in check_user_library_import_dir
safe_makedirs(os.path.join(self.app.config.user_library_import_dir, user.email))
File "lib/galaxy/util/path/__init__.py", line 114, in safe_makedirs
makedirs(path)
File "/hpc/software/installed/galaxy/20.01/.venv/lib64/python3.6/os.py", line 220, in makedirs
mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/home/sandra(a)mcri.edu.au'
Here is the auth_conf.xml:
<?xml version="1.0"?>
<auth>
<authenticator>
<type>PAM</type>
<options>
<auto-register>True</auto-register>
<maildomain>mcri.edu.au</maildomain>
<login-use-username>True</login-use-username>
<pam-service>sshd</pam-service>
</options>
</authenticator>
</auth>
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?
Thanks,
Sandra Maksimovic
Systems Administrator
Information Technology
Murdoch Children's Research Institute
The Royal Children's Hospital, 50 Flemington Road
Parkville, Victoria 3052 Australia
T +61 3 8341 6498
E sandra.maksimovic(a)mcri.edu.au<mailto:sandra.maksimovic@mcri.edu.au>
W mcri.edu.au<https://www.mcri.edu.au/>
Disclaimer
This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.
1 year, 7 months
Upload bed files seems to be hung
by Jean Jasinski
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?
Thanks,
Jean Jasinski
1 year, 7 months
Checkboxes issue (could not find an answer in the forum)
by fma＠intomics.com
Dear all,
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>
</div>
</div>
</div>
1 year, 8 months
James Taylor Foundation
by Dave Clements
Hello all,
The recent passing of Dr. James Taylor, the Ralph S. O’Connor Professor of
Biology and Professor of Computer Science at Johns Hopkins University, has
left an enormous void in the field of computational biology. To help fill
this void and continue James’ efforts, the Galaxy community has established
a memorial foundation in James’ name.
James believed that scientific progress can best be sustained through
mentoring of students and junior faculty. The Junior Training and
Educational Connections Hotspot (JTech) foundation will ensure
implementation of this vision. To begin, JTech will (1) support graduate
students to participate in computational biology and data science
conferences, and (2) organize and host mentoring sessions between senior
and junior faculty members at high-profile meetings. JTech will later
expand its reach as a platform for academic mentorship including high
school through college age students.
To make this happen we are accepting contributions here
https://galaxyproject.org/jxtx/.
Please, help us continue what James has started.
Thank you,
Dave C on behalf of the Galaxy Community
--
https://galaxyproject.org/
1 year, 8 months
May News: James Taylor, BCC2020 Abstracts Close Friday, and much, much more.
by Dave Clements
Hello all,
This is our first newsletter since January.
It has been an eventful and sorrowful four months for the world, and for
the Galaxy Community too: This newsletter starts with the tragic loss of
James Taylor, one of Galaxy’s founders and leaders. We lost James at the
beginning of April. This community, I suspect, will always feel that loss.
The May 2020 issue
https://galaxyproject.org/news/2020-05-galaxy-update/
James Peter Taylor , 1979-2020
* BCC2020 will be online, global, affordable, and accessible
* All abstracts are due May 8
* Galaxy COVID-19 Response
* Upcoming events
* Blog posts
* Galaxy Platform News
* Training material and doc updates
* Who’s Hiring
* New Releases
* New publications (671 of them)
* And other cool news too
If you have anything to include to next month’s newsletter, then please
send it to outreach(a)galaxyproject.org.
Thanks, for everything,
Dave C
--
https://galaxyproject.org/
1 year, 8 months
