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
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Hi,
I am struggling with the FTP connection on our local instance.
I start ProFTPd for SHA1 like this:
$ service proftpd start #the conf file is below
Notes: I had to do that as root, not possible as the non-root galaxy user
ROOT PRIVS: unable to seteuid(): Operation not permitted
-> is it possible to run proftpd as non-root?
The server run, but I am not able to connect with FTP -FileZilla (localhost:2021)
Log: Statut : Résolution de l'adresse de localhost
Statut : Connexion à [::1]:2021...
Statut : Échec de la tentative de connexion avec "ECONNREFUSED - Connexion refusée par le serveur", essai de l'adresse suivante.
Statut : Connexion à 127.0.0.1:2021...
Statut : Échec de la tentative de connexion avec "ECONNREFUSED - Connexion refusée par le serveur".
Erreur : Impossible d'établir une connexion au serveur
Statut : Attente avant nouvel essai...
Notes: The local instance doesn't have a proxy, I access it with ssh. (ssh -C -L 8081:localhost:8081 durandal).
Any ideas? Is it linked to the firewall?
Thanks,
Luc
#proftpd.conf
$cat /etc/proftpd.conf
# Basics, some site-specific
ServerName "Public Galaxy FTP"
ServerType standalone
DefaultServer on
Port 21
Umask 077
SyslogFacility DAEMON
SyslogLevel debug
MaxInstances 30
# This User & Group should be set to the actual user and group name which matche the UID & GID you will specify later in the SQLNamedQuery.
User nobody
Group nobody
DisplayConnect /etc/opt/local/proftpd_welcome.txt
# Passive port range for the firewall
PassivePorts 30000 40000
# Cause every FTP user to be "jailed" (chrooted) into their home directory
DefaultRoot ~
# Automatically create home directory if it doesn't exist
CreateHome on dirmode 700
# Allow users to overwrite their files
AllowOverwrite on
# Allow users to resume interrupted uploads
AllowStoreRestart on
# Bar use of SITE CHMOD
<Limit SITE_CHMOD>
DenyAll
</Limit>
# Bar use of RETR (download) since this is not a public file drop
<Limit RETR>
DenyAll
</Limit>
# Do not authenticate against real (system) users
AuthPAM off
# General database support (http://www.proftpd.org/docs/contrib/mod_sql.html)
#SQL module
LoadModule mod_sql.c
# Support for base-64 or hex encoded MD5 and SHA1 passwords from SQL tables
# (contrib/mod_sql_passwd.html)
LoadModule mod_sql_passwd.c
# Postgresql support (requires proftpd-postgresql package)
# (http://www.proftpd.org/docs/contrib/mod_sql.html)
LoadModule mod_sql_postgres.c
# set Authentication order
AuthOrder mod_sql.c
# Set this if Galaxy user UID and/or GID are less than 999
SQLMinID 400
# Common SQL authentication options
SQLEngine on
SQLPasswordEngine on
SQLBackend postgres
SQLConnectInfo postgres@localhost:5432 galaxyftp <dbpassword>
SQLAuthenticate users
##
# Set up mod_sql/mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1
SQLAuthTypes SHA1
SQLPasswordEncoding hex
# An empty directory in case chroot fails
#SQLDefaultHomedir /var/opt/local/proftpd
# Define a custom query for lookup that returns a passwd-like entry. Replace 512s with the UID and GID of the user running the Galaxy server
SQLUserInfo custom:/LookupGalaxyUser
SQLNamedQuery LookupGalaxyUser SELECT "email,password,512,512,'/home/nate/galaxy_dist/database/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'"
------------
Luc Cornet, PhD
Bio-informatician
Mycology and Aerobiology
Sciensano
Hi galaxy community,
I am quite new in galaxy but I would like to install a local instance on our cluster (SGE).
I have a problem with DRMAA :
When I activate the --daemon mode, the job don't pass in the queue system but with no Damon, it pass (the log below)
The second problem is that $GALAXY_SLOTS is not define, Could it be related to the problem below ?
Someone can help me, please ? (available at : https://help.galaxyproject.org/t/job-submission-failed-when-daemon/351)
Thanks,
Luc
## with no daemon
galaxy.jobs.runners.drmaa DEBUG 2020-04-28 17:07:21,424 [p:32191,w:1,m:0] [DRMAARunner.work_thread-1] (47) submitting file /media/vol2/home/galaxy/galaxy/database/jobs_directory/000/47/galaxy_47.sh
galaxy.jobs.runners.drmaa DEBUG 2020-04-28 17:07:21,425 [p:32191,w:1,m:0] [DRMAARunner.work_thread-1] (47) native specification is: -q cassava.q -pe snode 10
galaxy.jobs.runners.drmaa INFO 2020-04-28 17:07:21,440 [p:32191,w:1,m:0] [DRMAARunner.work_thread-1] (47) queued as 1007701
galaxy.jobs DEBUG 2020-04-28 17:07:21,441 [p:32191,w:1,m:0] [DRMAARunner.work_thread-1] (47) Persisting job destination (destination id: big_jobs)
galaxy.jobs.runners.drmaa DEBUG 2020-04-28 17:07:22,042 [p:32191,w:1,m:0] [DRMAARunner.monitor_thread] (47/1007701) state change: job is queued and active
## with daemon
galaxy.jobs.runners.drmaa DEBUG 2020-04-28 15:39:16,138 [p:26779,w:1,m:0] [DRMAARunner.work_thread-1] (45) submitting file /media/vol2/home/galaxy/galaxy/database/jobs_directory/000/45/galaxy_45.sh
galaxy.jobs.runners.drmaa DEBUG 2020-04-28 15:39:16,138 [p:26779,w:1,m:0] [DRMAARunner.work_thread-1] (45) native specification is: -q cassava.q -pe snode 10
## job_conf
<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is
configured by default (if there is no explicit config). -->
<job_conf>
<plugins>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
<plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
<param id="drmaa_library_path">/media/vol1/gridengine/lib/linux-x64/libdrmaa.so</param>
</plugins>
<destinations default="local">
<destination id="local" runner="local"/>
<destination id="big_jobs" runner="drmaa">
<param id="nativeSpecification">-q cassava.q -pe snode 10</param>
</destination>
</destinations>
<tools>
<tool id="maker" destination="big_jobs" />
<tool id="metaspades" destination="big_jobs" />
</tools>
</job_conf>
------------
Luc Cornet, PhD
Bio-informatician
Mycology and Aerobiology
Sciensano
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*Call for Participation:* Gateways 2020 (October 19–21, Bethesda,
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*What’s a gateway?* Gateways are user-friendly interfaces to computing,
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research environments, eScience, virtual labs, eResearch, digital
repositories, or research cyberinfrastructure.
*Deadlines:*
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Read more details in the *Call for Participation*:
http://sciencegateways.org/gateways2020/call
<https://urldefense.com/v3/__http://sciencegateways.org/gateways2020/call__;…>
/*COVID-19 UPDATE:*
Because the COVID-19 outbreak is changing rapidly, we are continuing to
plan our October conference while monitoring the situation. In case we
have to cancel, we will strive to offer an alternative format, and
peer-reviewed, accepted submissions would still be published in the
Gateways 2020 Proceedings. Questions, concerns, and suggestions may be
sent to help(a)sciencegateways.org <mailto:help@sciencegateways.org>./
*
Call for Participation: Gateways 2020(October 19–21, Bethesda, Maryland)
is now accepting submissions of short papers, demos, panels, tutorials,
and workshops on the topic of gateways for science, engineering, or
other disciplines.
What’s a gateway?Gateways are user-friendly interfaces to computing,
data, instruments, and other domain-specific resources to support
research and education. They may also be known as portals, virtual
research environments, eScience, virtual labs, eResearch, digital
repositories, or research cyberinfrastructure.
Popular topics include:
*
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or best practices
*
Educational topics (tutorials, demos) directed toward the next
generation of gateway creators as well as gateways used for education
*
Any other aspect interesting to fellow gateway creators or users,
such as emerging capabilities, approaches or technologies
Learning Labs(impromptu group discussions and gatherings) will also be
welcoming early submissions as well as on-site proposed topics.Deadlines:
*
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COVID-19 interruptions)
*
Short Papers, Demos, and Panels: May 11
*
Posters (open to all attendees): September 11
Read more details in the Call for
Participation:http://sciencegateways.org/gateways2020/call
COVID-19 UPDATE:
Because the COVID-19 outbreak is changing rapidly, we are continuing to
plan our October conference while monitoring the situation. In case we
have to cancel, we will strive to offer an alternative format, and
peer-reviewed, accepted submissions would still be published in the
Gateways 2020 Proceedings. Questions, concerns, and suggestions may be
sent to help(a)sciencegateways.org <mailto:help@sciencegateways.org>.
*