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May News: James Taylor, BCC2020 Abstracts Close Friday, and much, much more.
by Dave Clements 04 May '20

04 May '20

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/

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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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BCC2020 meeting will be held online
by Dave Clements 24 Mar '20

24 Mar '20

Hello all, The Organizing Committee of the 2020 Bioinformatics Community Conference (BCC2020, https://bcc2020.github.io/) has come to the difficult decision to hold the conference online. We are making this decision after much consideration of the ongoing spread of COVID-19, striving to take the most socially responsible action while maintaining a forum in which our community can share their work and discovery. It is hard to predict what things will look like in July, but given current reports and models, it seems unlikely that the situation will be back to “business as usual”. We also considered that, even if some people were able to attend, it is possible that many people would still find it difficult to travel to Toronto. We believe that making this decision now will allow us to focus on organizing an engaging conference in this new format. We will be inviting our community to engage in new ways, and hope that BCC2020 will be an important space for discussion for the Open Source bioinformatics community. The virtual meeting will still take place as planned, on July 18-21. There will be opportunities for training before the main meeting, and a CollaborationFest starting on July 22. We are discussing how to arrange the schedule to allow for participation across the globe; more details will be coming soon. Registration will open in a few weeks, and fees will be lower than for an in-person meeting. The abstract submission deadline has been postponed to April 30th. Abstracts will follow the usual submission and review processes. There are many details to be worked out – for example, a meeting schedule that takes into account time zones, videoconferencing technology, ways to enrich our online interactions (while acknowledging that nothing can replace the vital social interaction that in-person meetings provide), etc. Many of these aspects are new for us too; we welcome your input, particularly if you have suggestions about how to make our first Virtual Bioinformatics Community Conference a success. We are looking forward to exploring this new meeting format, and we hope you will join us. Stay well, BCC2020 Organizers -- https://galaxyproject.org/

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SAML Authentication
by Keith Suderman 16 Mar '20

16 Mar '20

We are (finally) adding SAML authentication to our Galaxy instance so users can authenticate with EduGain (EU) or InCommon (US). While doing some searching I found an article that says, "Galaxy supports LDAP, SAML and now OIDC (see https://galaxyproject.org/authnz/ <https://galaxyproject.org/authnz/>)." [1] Looking at the release_20.01 code I see lots has changed in respect to authorization (we are still using 19.01 so I am glad I looked), but I don't see anything related to SAML. I am not finding anything in the documentation either. I am missing something or am I looking in the wrong place(s)? I was expecting (hoping) to see a saml.py in /lib/galaxy/auth/providers/ or something similar. I do have Shibboleth authentication working using Apache and mod_shib in front of Galaxy, but that requires everyone to be able to authenticate and we would still like to allow anonymous access. Ideally users that don't have InCommon/EduGain access would still be able to create local accounts as well. Before I start hacking around trying to create an authentication plugin for Galaxy I wanted to check to see if there was any other ongoing work in the same area. There is an old issue on GitHub [2], but I can't find anything else related. I see the OIDC stuff uses social-auth, which does include a SAML backend. Social-auth just uses the python3-saml package and I already have a simple client that uses python3-saml for authentication so I am hoping a saml plugin will be "Relatively Easy" (TM). Thanks, Keith 1. https://academic.oup.com/bioinformatics/article/36/1/1/5514039 2. https://github.com/galaxyproject/galaxy/issues/3146

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BCC2020 registration postponed due to COVID-19 uncertainty
by Dave Clements 09 Mar '20

09 Mar '20

Hello all, We are postponing opening registration for the 2020 Bioinformatics Community Conference (BCC2020). See the announcement for details. https://bcc2020.github.io/blog/postponement Dave C, on behalf of the BCC2020 Organizers. -- https://galaxyproject.org/

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Error keeps occuring
by Hill-Spanik, Kristina M 28 Feb '20

28 Feb '20

Hi, I keep getting the following error. Any help would be appreciated. Thanks, Kristy ________________________ Kristina Hill-Spanik Lab Manager Molecular Biology Core Facility Grice Marine Lab College of Charleston 205 Fort Johnson Road Charleston, SC 29412 hillkm1(a)cofc.edu<mailto:hillkm1@cofc.edu> 843-953-9193 An error occurred while updating information with the server. Please contact a Galaxy administrator if the problem persists. { "userAgent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_6) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/13.0.5 Safari/605.1.15", "onLine": true, "version": "20.01", "xhr": { "readyState": 4, "responseText": "{\"err_msg\": \"Uncaught exception in exposed API method:\", \"err_code\": 0}", "responseJSON": { "err_msg": "Uncaught exception in exposed API method:", "err_code": 0 }, "status": 500, "statusText": "Internal Server Error" }, "options": { "validate": true, "parse": true, "method": "delete", "emulateHTTP": false, "emulateJSON": false, "textStatus": "error", "errorThrown": "Internal Server Error" }, "url": "https://usegalaxy.org/history/view_multipl/api/histories/a07a6d267500b6b2/c…", "data": { "collection_type": "list:paired", "deleted": true, "history_content_type": "dataset_collection", "model_class": "HistoryDatasetCollectionAssociation", "populated_state_message": null, "job_source_id": "80374338f06ac04b", "history_id": "a07a6d267500b6b2", "type": "collection", "job_source_type": "ImplicitCollectionJobs", "hid": 3371, "type_id": "dataset_collection-e6d871d8a2cf90c0", "tags": [], "update_time": "2020-02-26T14:05:47.592Z", "name": "FastQC on collection 3370: Webpage", "visible": true, "url": "/api/histories/a07a6d267500b6b2/contents/dataset_collections/e6d871d8a2cf90c0", "populated_state": "new", "id": "e6d871d8a2cf90c0", "create_time": "2020-02-26T14:05:47.592Z", "element_count": 153, "recursive": true, "purge": true, "elements": [] }, "model": { "collection_type": "list:paired", "deleted": true, "history_content_type": "dataset_collection", "model_class": "HistoryDatasetCollectionAssociation", "populated_state_message": null, "job_source_id": "80374338f06ac04b", "history_id": "a07a6d267500b6b2", "type": "collection", "job_source_type": "ImplicitCollectionJobs", "hid": 3371, "type_id": "dataset_collection-e6d871d8a2cf90c0", "tags": [], "update_time": "2020-02-26T14:05:47.592Z", "name": "FastQC on collection 3370: Webpage", "visible": true, "url": "/api/histories/a07a6d267500b6b2/contents/dataset_collections/e6d871d8a2cf90c0", "populated_state": "new", "id": "e6d871d8a2cf90c0", "create_time": "2020-02-26T14:05:47.592Z", "element_count": 153, "recursive": true, "purge": true, "elements": [] }, "user": { "id": "962c63e5584bc3ea", "username": "khillspanik", "total_disk_usage": 49650284207, "nice_total_disk_usage": "46.2 GB", "quota_percent": 18, "is_admin": false, "preferences": {}, "model_class": "User", "deleted": false, "active": true, "last_password_change": "2019-12-05T14:12:35.446534", "tags_used": [] } }

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