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***UNCHECKED*** Nextflow within galaxy
by Luc Cornet 08 Jul '20

08 Jul '20

Hi everyone, I would like to run a Netxflow script in galaxy (yes I know it’s strange). So I made a test but I have a problem that I don’t undertstand, I am able to launch my Nextflow tool in galaxy but not to complete the analysis. The log out of galaxy : > juil.-07 19:28:53.888 [main] DEBUG nextflow.Session - Work-dir: /Users/luc/Documents/Programs/galaxy/database/jobs_directory/000/24/working/work [Mac OS X] juil.-07 19:28:53.888 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/luc/Documents/Programs/galaxy/tools/BCCM-tools/bin juil.-07 19:28:53.988 [main] DEBUG nextflow.Session - Session start invoked juil.-07 19:28:54.296 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution juil.-07 19:28:54.368 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null juil.-07 19:28:54.368 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' juil.-07 19:28:54.372 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local juil.-07 19:28:54.375 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=4; memory=16 GB; capacity=4; pollInterval=100ms; dumpInterval=5m juil.-07 19:28:54.446 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Testo -- maxForks: 4 juil.-07 19:28:54.477 [main] DEBUG nextflow.script.ScriptRunner - > Await termination juil.-07 19:28:54.477 [main] DEBUG nextflow.Session - Session await juil.-07 19:28:54.579 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run juil.-07 19:28:54.584 [Task submitter] INFO nextflow.Session - [37/23b693] Submitted process > Testo juil.-07 19:28:54.647 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: Testo; status: COMPLETED; exit: 0; error: -; workDir: /Users/luc/Documents/Programs/galaxy/database/jobs_directory/000/24/working/work/37/23b693d7b8dbbf227f19b3dd9780a7] juil.-07 19:28:54.674 [main] DEBUG nextflow.Session - Session await > all process finished juil.-07 19:28:54.675 [main] DEBUG nextflow.Session - Session await > all barriers passed juil.-07 19:28:54.682 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=1; failedCount=0; ignoredCount=0; cachedCount=0; succeedDuration=6ms; failedDuration=0ms; cachedDuration=0ms] juil.-07 19:28:54.855 [main] DEBUG nextflow.CacheDB - Closing CacheDB done juil.-07 19:28:54.869 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye And the log in galaxy: > juil.-08 11:38:09.834 [main] DEBUG nextflow.Session - Work-dir: /Users/luc/Documents/Programs/galaxy/database/jobs_directory/000/27/working/work [Mac OS X] juil.-08 11:38:09.834 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/luc/Documents/Programs/galaxy/tools/BCCM-tools/bin juil.-08 11:38:10.001 [main] DEBUG nextflow.Session - Session start invoked juil.-08 11:38:10.373 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution juil.-08 11:38:10.450 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null juil.-08 11:38:10.450 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' juil.-08 11:38:10.455 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local juil.-08 11:38:10.458 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=4; memory=16 GB; capacity=4; pollInterval=100ms; dumpInterval=5m juil.-08 11:38:10.534 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Testo -- maxForks: 4 juil.-08 11:38:10.591 [main] DEBUG nextflow.script.ScriptRunner - > Await termination Can someone help me with this ? Best, Luc ------------ Luc Cornet, PhD Bio-informatician Mycology and Aerobiology Sciensano

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July Galaxy News: BCC2020 Deadlines, Schedule, Fellowships; Galaxy Dev Roundtable, ...
by Dave Clements 01 Jul '20

01 Jul '20

The July 2020 Galaxy News is here: https://galaxyproject.org/news/2020-07-galaxy-update/ In the July 2020 Issue * BCC2020 starts July 17 * Early registration ends July 10 * BoF proposals due July 10 * Fellowships due July 5 * New Silver Sponsor: GalaxyWorks * Full training, talk, and poster/demo schedules are online * Galaxy and the NCBI Sequence Read Archive (SRA) * Upcoming events * Including the new Galaxy Developer Roundtable * Galaxy Platform News * Training material and doc updates * Who's Hiring * New blog posts * New Releases See you online in just over 2 weeks, Dave C -- https://galaxyproject.org/

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Release of Galaxy 20.05
by Marius van den Beek 30 Jun '20

30 Jun '20

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 20.05. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/20.05_announce.html and user facing release notes are at https://docs.galaxyproject.org/en/master/releases/20.05_announce_user.html. A few release highlights are: Many new Interactive Tools ------------------------------------ Galaxy interactive tools allow a greater depth of analysis via access to GUI-based tools inside an instance. 10 new interactive tools (some previously available only on the UseGalaxy.eu server) join the standard base toolset. Improvements to the Higlass interactive tool now also allow for a more in-depth visualization of multiple datasets in various formats simultaneously. Data Tables can now be backed by refgenie ---------------------------------------------------------- Refgenie manages storage, access, and transfer of reference genome resources. Galaxy can now fill data tables that were received from a refgenie installation. Tool Shed is now Python3 ready ------------------------------------------ As the last component in the Galaxy Codebase the Tool Shed has been ported to Python 3. This concludes a 4 year effort to port the Galaxy codebase to Python 3. Workflow Editor and Workflow Run Form in Vue.js ------------------------------------------------------------------ The Workflow Editor and Workflow Run Form have been re-written in Vue.js. While the functionality has been preserved this lays the groundwork for creating beautiful and reactive custom variants of these components in the future Accelerated Galaxy Startup ------------------------------------- Galaxy now caches expanded tool documents, delays creating the tool search index until after startup and creates search indexes incrementally Check out the release notes for a lot more details - there are many more enhancements such as social login, tool recommendations, visualizations, datatypes and bug fixes. Thanks for using Galaxy!

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June 2020 Galaxy News
by Dave Clements 11 Jun '20

11 Jun '20

Hello all, The June 2020 issue is hot off the presses: https://galaxyproject.org/news/2020-06-galaxy-update/ In this issue: - James Taylor Foundation - BCC2020 will be online, global, affordable, and accessible - Galaxy and the NCBI Sequence Read Archive (SRA) - Upcoming events - Galaxy Platform News - Training material and doc updates - Who's Hiring - New Releases - New publications - 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, Dave C -- https://galaxyproject.org/

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Galaxy with SELINUX
by Vipin TS 10 Jun '20

10 Jun '20

Dear Community, Is it possible to run the latest version of Galaxy on a SELINUX enabled machine? Thanks in advance! Vipin

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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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Upload bed files seems to be hung
by Jean Jasinski 27 May '20

27 May '20

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

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Checkboxes issue (could not find an answer in the forum)
by fma＠intomics.com 22 May '20

22 May '20

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>

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James Taylor Foundation
by Dave Clements 07 May '20

07 May '20

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/

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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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