April 2020 - galaxy-dev - lists.galaxyproject.org

pam login issue
by Sandra Maksimovic 29 May '20

29 May '20

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.

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FTP Local instance: ECONNREFUSED
by Luc Cornet 30 Apr '20

30 Apr '20

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

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Daemon mode fail job submission
by Luc Cornet 28 Apr '20

28 Apr '20

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"?>  <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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BCC2020 Abstract submission and Registration are open
by Dave Clements 27 Apr '20

27 Apr '20

2020 Bioinformatics Community Conference (BCC2020) Online, July 17-26 https://bcc2020.github.io/ The 2020 Bioinformatics Community Conference (BCC2020) will be online, global, affordable, and accessible to all. Key Dates: May 8: Deadline for submitting talk/poster abstracts (this will not be extended) June 6: Authors notified about talk/poster acceptance July 10: Early registration ends July 17-19: BCC2020 tutorials July 19-22: BCC2020 main meeting July 22-24, 24-26: CollaborationFest Core and Encore BCC2020 -> https://bcc2020.github.io/ BCC2020 is a joint event bringing together the BOSC and Galaxy Communities. If you are working in data intensive life science research then there will be no better event this year to share your work, and to learn from others. BCC2020 will be held July 17-26, and offer 2 days of training, a 3 day meeting, and a 4 day CollaborationFest. BCC2020 is Online -> https://bcc2020.github.io/blog/going-virtual All BCC2020 events will be held online. Training will be live and interactive. The meeting will feature keynotes, accepted talks, lightning talks, posters, demos, and birds-of-a-feather and other networking opportunities. Talks (with the possible exception of keynotes) will be pre-recorded. Posters, demos, and BoFs will be live and interactive. The CoFest will also be live and interactive. BCC2020 is Global -> https://bcc2020.github.io/blog/going-global BCC2020 events will be held twice: once in the originally scheduled Toronto time zone (BCC West), and then again 12 hours later in the Eastern hemisphere (BCC East). Training will differ between East and West, with enrollment open to all, regardless of where you are. The main conference content will be presented in both East and West. We are striving to have the CoFest run continuously, with participants from every part of the world. BCC2020 is Affordable -> https://bcc2020.github.io/Registration/ We have slashed registration rates for BCC2020, and are offering even larger discounts to participants based in low and lower-middle income countries. Pricing starts at US$3 per training session, and $12 for the 3 day meeting. The CoFest is free. BCC2020 is Accessible Going online and global, combined with the low registration rates make this the most accessible Galaxy and BOSC conference ever. If you work in open source bioinformatics then this is 2020’s best opportunity to share your work and learn from others. Abstracts Due May 8 -> https://bcc2020.github.io/submit/ BCC2020 is seeking oral presentations, lightning talks, posters, and demos, from researchers working in bioinformatics, and from all over the world. Abstracts are due May 8 (and that deadline will not be extended). Please submit your work today. Register Now -> https://bcc2020.github.io/Registration/ BCC2020 registration is now open. Registering early saves 50% off of the full rates. We hope to see you in July at BCC2020, BCC2020 Organizers -- https://galaxyproject.org/

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Gateways 2020 Call for Participation (Tutorials deadline extended to May 5)
by Katherine Lawrence 24 Apr '20

24 Apr '20

*Call for Participation:* Gateways 2020 (October 19–21, Bethesda, Maryland) is now accepting submissions. *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. *Deadlines:* * Tutorials and Workshops: extended to May 5 * 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 <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>./

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Gateways 2020 Call for Participation (Tutorials due Apr. 28; other formats due May 11)
by Katherine Lawrence 02 Apr '20

02 Apr '20

* 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: * Gateway design, use, impact, development processes, sustainability, 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: * Tutorials and Workshops: April 28 (new deadline to accommodate 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>. *

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