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Error keeps occuring
by Hill-Spanik, Kristina M 29 Feb '20

29 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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Release of Galaxy 20.01
by Marius van den Beek 28 Feb '20

28 Feb '20

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 20.01. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/20.01_announce.html and user facing release notes are at https://docs.galaxyproject.org/en/master/releases/20.01_announce_user.html. A few release highlights are: Workflow Executions Menu ------------------------ This menu can be reached from the User menu -> Workflow Invocations and lists your recent Workflow executions, their status and links to the Workflow Editor and the History with the results of the Workflow run. Enhanced workflow functionality ------------------------------- Workflows can now make use of optional datasets and optional parameters, optional parameter default values and dataset inputs can now be restricted to user-defined datatypes. The workflow editor and execution engine have been enhanced to allow defining options to choose from, and these options can be connected to compatible text, integer, float, color and select tool parameters for more flexible and universally reusable workflows Galay Markdown Pages and Workflow Reports as PDF ------------------------------------------------ An additional link has been added to Galaxy Markdown Pages and Workflow reports that exports your document as a standalone PDF. Screen Reader friendly Navigation -------------------------------- The top menu and the Workflow Editor have been improved for easier navigation using Screen Readers and the Keyboard. Email-notification for completed jobs ------------------------------------- You can now select to be notified by email when a tool run has finished. Check out the release notes for a lot more details - there are many more enhancements such as new interface elements, visualizations, datatypes and bug fixes as well as instructions for upgrading your Galaxy installation to Python 3. Thanks for using Galaxy!

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issues file uploading
by Thomas BOUTET 27 Feb '20

27 Feb '20

Hello, I have issues uplaoding .bed data on galaxeast. I am sure the data and format is fine as I am able to upload the same file in Galaxy. Yesterday I uploaded several .bed files and everything works fine. As I didn’t reach my quota (90GB) I am sure this is not the problem. Thank you very much for your help.

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Fwd: [GMOD-devel] GMOD in Google Summer of Code
by Dave Clements 21 Feb '20

21 Feb '20

Hi All, Scott's "But WAIT!" comment applies to Galaxy too. :-) See below if you have an idea. Cheers, Dave C ---------- Forwarded message --------- From: Scott Cain <scott(a)scottcain.net> Date: Thu, Feb 20, 2020 at 6:16 PM Subject: [GMOD-devel] GMOD in Google Summer of Code To: gmod-announce <gmod-announce(a)lists.sourceforge.net>, gmod-ajax < gmod-ajax(a)lists.sourceforge.net>, gmod tripal devel < gmod-tripal-devel(a)lists.sourceforge.net>, Gbrowse (E-mail) < gmod-gbrowse(a)lists.sourceforge.net>, GMOD Schema/Chado List < gmod-schema(a)lists.sourceforge.net>, gmod-devel < gmod-devel(a)lists.sourceforge.net>, <apollo(a)lbl.gov>, maker-devel(a)yandell-lab.org List <maker-devel(a)yandell-lab.org> Hello, I am very pleased to announce that GMOD in conjunction with Reactome, Galaxy and OICR/WormBase, together forming Open Genome Informatics, has been accepted for the Google Summer of Code. If you or someone you know might be a student interested in participating in GSoC, please take a look at http://gmod.org/wiki/GSOC_Project_Ideas_2020 where there are proposed projects that cover a fair number of technologies. Official proposals from students will be due in mid March (more on that later). But WAIT! There's more: if you might be interested in being a mentor and working with a student this summer, it's not too late! You can add new project ideas to the page above (contact me if you need an account), or you can even volunteer to add yourself to one of the existing ideas as a potential mentor. Please feel free to forward this to other mailing lists or people who might be interested. We are already an eclectic, dispersed group, so everyone is welcome. Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research _______________________________________________ Gmod-devel mailing list Gmod-devel(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/gmod-devel -- https://galaxyproject.org/

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Installing from toolshed
by Omar Ali 12 Feb '20

12 Feb '20

I am trying to install the denovo RNA seq tools to galaxy from the toolshed ( https://toolshed.g2.bx.psu.edu/ ) but it is not allowing me to. can you assist please. -- Regards, Omar Ali. B.Sc. Biology & Environmental and Natural Resource Management (2012-2015) M.Phil. Microbiology (2015-2018) Ph.D. Microbiology Candidate (2018- present) U.W.I. #Remember to always help those in need. #Always be brave and have courage

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BCC2020 Training Topic Voting is Open
by Dave Clements 12 Feb '20

12 Feb '20

Hello all, The The Bioinformatics Community Conference (BCC2020) <https://bcc2020.github.io/>, will bring together the Galaxy Community Conference (GCC) and the Bioinformatics Open Source Conference (BOSC) in Toronto, Canada in July 2020, following ISMB 2020 <https://www.iscb.org/ismb2020> in Montréal. BCC2020 will start with a dedicated training day, followed by 3 days of mixed meeting and training events. The community (you!) determines what training will be offered at BCC2020. *Nominations from the community <https://bcc2020.github.io/training/>* are now ready for review and voting. If you are possibly attending BCC2020 then please take a few minutes to review the nominations and then submit your ballot <https://docs.google.com/forms/d/e/1FAIpQLSfmOowsHt0cL1ukiGvOdh7WxWKoSuT-3GM…>. Voting closes on February 21. Thanks in advance for your input, and we hope to see you in Toronto, BCC2020 Organizers -- https://galaxyproject.org/

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Errors running jobs in Galaxy 16.01 with slurm-drmaa 1.1.0
by Philip Blood 29 Jan '20

29 Jan '20

Hi Folks, I'm trying to get an old instance of Galaxy (16.01) working for a user who needs to use it this week for a class he is teaching (so upgrading Galaxy is not an option at the moment). Due to a recent slurm upgrade on our compute system to slurm 18.08.8, we had to replace the old slurm-drmaa 1.0.7 library <http://apps.man.poznan.pl/trac/slurm-drmaa>, which doesn't work with with 18.08.8, with Nate's forked slurm-drmaa library version 1.1.0 <https://github.com/natefoo/slurm-drmaa>. That built fine with slurm 18.08.8 and (I think) we updated all the relevant pointers in the galaxy config to point to the new slurm-drmaa 1.1.0 library. However, now when I try to run jobs on our system I get errors (it worked fine before with slurm-drmaa 1.0.7 and the older version of slurm). So, I wanted to get a quick sanity check on whether this might be an issue with trying to use the new slurm-drmaa with an old version of Galaxy, 16.01, or if anyone has any other quick thoughts on troubleshooting this. The errors I get are below. Best, Phil *Short version (just the errors):* 198.91.54.159 - - [31/Aug/2019:16:31:28 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:30,366 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (2): No such file or directory* 198.91.54.159 - - [31/Aug/2019:16:31:32 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:35,372 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:37 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:40,377 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:41 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:45 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:45,383 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:49 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:50,388 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:53 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa ERROR 2019-08-31 16:31:55,393 (10) All attempts to submit job failed * *Full context:* 198.91.54.159 - - [31/Aug/2019:16:30:27 +0000] "GET /api/tools/squeue/build HTTP/1.1" 200 - "https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" galaxy.tools DEBUG 2019-08-31 16:30:30,142 Validated and populated state for tool request (4.081 ms) galaxy.tools.actions INFO 2019-08-31 16:30:30,285 Handled output (100.616 ms) galaxy.tools.actions INFO 2019-08-31 16:30:30,319 Verified access to datasets (0.005 ms) galaxy.tools.execute DEBUG 2019-08-31 16:30:30,368 Tool [squeue] created job [10] (206.086 ms) galaxy.tools.execute DEBUG 2019-08-31 16:30:30,376 Executed all jobs for tool request: (233.862 ms) 198.91.54.159 - - [31/Aug/2019:16:30:30 +0000] "POST /api/tools HTTP/1.1" 200 - "https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:30:30 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" galaxy.jobs DEBUG 2019-08-31 16:30:30,747 (10) Working directory for job is: /opt/packages/galaxy/galaxy01/database/job_working_directory/000/10 galaxy.jobs.handler DEBUG 2019-08-31 16:30:30,751 (10) Dispatching to slurm runner galaxy.jobs DEBUG 2019-08-31 16:30:30,774 (10) Persisting job destination (destination id: LM4) galaxy.jobs.runners DEBUG 2019-08-31 16:30:30,790 Job [10] queued (38.578 ms) galaxy.jobs.handler INFO 2019-08-31 16:30:30,818 (10) Job dispatched galaxy.tools.deps DEBUG 2019-08-31 16:30:31,012 Building dependency shell command for dependency 'slurm' galaxy.tools.deps DEBUG 2019-08-31 16:30:31,013 Find dependency slurm version None galaxy.tools.deps DEBUG 2019-08-31 16:30:31,013 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x1b38390> (isnull? True) galaxy.tools.deps DEBUG 2019-08-31 16:30:31,014 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x7fc78c334750> (isnull? False) galaxy.jobs.command_factory INFO 2019-08-31 16:30:31,057 Built script [/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/tool_script.sh] for tool command[PACKAGE_BASE=/opt/packages/galaxy/galaxy01/tool_dependencies/slurm/18.08.8; export PACKAGE_BASE; . /opt/packages/galaxy/galaxy0 1/tool_dependencies/slurm/18.08.8/env.sh; echo "hostname:" > output; echo " " >> output; hostname >> output; echo " " >> output; env >> output; echo " " >> output; date >> output; echo " " >> output; echo "Uptime:" >> output; echo " " >> output; uptime >> output; echo " " >> output; echo "Module s:" >> output; echo " " >> output; module avail >> output 2>&1; echo " " >> output; echo "SLURM Queue Status" >> output; echo " " >> output; echo "If your job is running on the queues, it will be listed in the reports below:" >> output; echo " " >> output; echo " " >> output; echo "Normal Report: s queue" >> output; echo " " >> output; echo " " >> output; echo " " >> output; squeue >> output; date >> output; echo " " >> output; echo " " >> output; echo "*** Full Report: squeue -l ***" >> output; echo " " >> output; squeue -l >> output; echo " " >> output; echo " " >> output; date >> output; echo " " >> output; echo "Local: ${LOCAL}" >> output; echo "Ramdisk: ${RAMDISK}" >> output; workdir=`pwd`; echo "workdir is $workdir" >> output; cd $LOCAL; echo "i am in `pwd`" >> $workdir/output; cd $workdir; echo "i am in `pwd`" >> output; date >> output; echo " " >> output] galaxy.tools.deps DEBUG 2019-08-31 16:30:31,259 Building dependency shell command for dependency 'samtools' galaxy.tools.deps DEBUG 2019-08-31 16:30:31,259 Find dependency samtools version None galaxy.tools.deps DEBUG 2019-08-31 16:30:31,259 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x1b38390> (isnull? True) galaxy.tools.deps DEBUG 2019-08-31 16:30:31,279 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x7fc7b01e01d0> (isnull? False) galaxy.jobs.runners DEBUG 2019-08-31 16:30:31,284 (10) command is: /opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/tool_script.sh; return_code=$?; if [ -f /opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/output ] ; then cp /opt/packages/galaxy/galaxy01/databas e/job_working_directory/000/10/output /opt/packages/galaxy/galaxy01/database/files/000/dataset_10.dat ; fi; PACKAGE_BASE=/opt/packages/galaxy/galaxy01/tool_dependencies/samtools/0.1.19; export PACKAGE_BASE; . /opt/packages/galaxy/galaxy01/tool_dependencies/samtools/0.1.19/env.sh; python "/opt/packa ges/galaxy/galaxy01/database/job_working_directory/000/10/set_metadata_jGYkkM.py" "/opt/packages/galaxy/galaxy01/tmp/tmpxmB5GA" "/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/galaxy.json" "/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/metadata_in_HistoryD atasetAssociation_10_u2k7qq,/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/metadata_kwds_HistoryDatasetAssociation_10_2ZmSXR,/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/metadata_out_HistoryDatasetAssociation_10_shC78c,/opt/packages/galaxy/galaxy01/databa se/job_working_directory/000/10/metadata_results_HistoryDatasetAssociation_10_57x96D,/opt/packages/galaxy/galaxy01/database/files/000/dataset_10.dat,/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/metadata_override_HistoryDatasetAssociation_10_AEeOfc" 5242880; sh -c "exit $retur n_code" galaxy.jobs.runners.drmaa DEBUG 2019-08-31 16:30:31,356 (10) submitting file /opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/galaxy_10.sh galaxy.jobs.runners.drmaa DEBUG 2019-08-31 16:30:31,356 (10) native specification is: -p LM -C LM -N 1 -n 4 --ntasks-per-node=4 --mem=192500 -t 24:00:00 198.91.54.159 - - [31/Aug/2019:16:30:34 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:30:38 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:30:42 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:30:47 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:30:51 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:30:55 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:30:59 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:03 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:08 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:12 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:16 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:20 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:24 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:28 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:30,366 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (2): No such file or directory* 198.91.54.159 - - [31/Aug/2019:16:31:32 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:35,372 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:37 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:40,377 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:41 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:45 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:45,383 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:49 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:50,388 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:53 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa ERROR 2019-08-31 16:31:55,393 (10) All attempts to submit job failed *

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[GSoC 2020] [Open Genome Informatics] Google Summer of Code 2020 Participation
by Robin Haw 29 Jan '20

29 Jan '20

Dear All, The Open Genome Informatics team serves as an “umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC)<https://summerofcode.withgoogle.com/>. Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others. Call for 2020 Project Ideas and Mentors: We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2020>. For more information please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC#Google_Summer_of_Code_2020>. The mentoring organization application deadline with GSoC is February 5th at 2 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible. Please forward this to others who might be interested in taking part. If you have any questions please let us know. Thanks, Robin, Marc, Dave, Dannon, and Scott. Robin Haw, PhD Reactome | JBrowse - Senior Project Manager and Outreach Co-ordinator robin.haw(a)oicr.on.ca<mailto:robin.haw@oicr.on.ca> Ontario Institute for Cancer Research MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3 @OICR_news | www.oicr.on.ca | @reactome | reactome.org | @JBrowseGossip | jbrowse.org Collaborate. Translate. Change lives. This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

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[GSoC 2020] [Open Genome Informatics] Google Summer of Code 2020 Participation
by Robin Haw 29 Jan '20

29 Jan '20

Dear All, Sorry for the multiple postings! The Open Genome Informatics team serves as an “umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC)<https://summerofcode.withgoogle.com/>. Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others. Call for 2020 Project Ideas and Mentors: We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2020>. For more information please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC#Google_Summer_of_Code_2020>. The mentoring organization application deadline with GSoC is February 5th at 2 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible. Please forward this to others who might be interested in taking part. If you have any questions please let us know. Thanks, Robin, Marc, Dave, Dannon, and Scott. Robin Haw, PhD Reactome | JBrowse - Senior Project Manager and Outreach Co-ordinator robin.haw(a)oicr.on.ca<mailto:robin.haw@oicr.on.ca> Ontario Institute for Cancer Research MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3 @OICR_news | www.oicr.on.ca | @reactome | reactome.org | @JBrowseGossip | jbrowse.org Collaborate. Translate. Change lives. This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

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LDA Effect Size (LEfSE) error
by Caroline Kelsey 24 Jan '20

24 Jan '20

Hello, First of all thank you for all of your hard work developing such an informative and intuitive tool. I have been successful in running the LEfSE analyses for some of my data, but unfortunately, for the majority I get an error message when it comes to the step where the Effect size is calculated. The error message is copied below: /galaxy_venv/local/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning: Error in (function (file = "", n = NULL, text = NULL, prompt = "?", keep.source = getOption("keep.source"), : <text>:1:47: unexpected numeric constant 1: effect.size <- abs(mean(LD[sub_d[,"class"]==""1 ^ warnings.warn(x, RRuntimeWarning) Traceback (most recent call last): File "/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/run_lefse.py", line 89, in <module> if params['rank_tec'] == 'lda': lda_res,lda_res_th = test_lda_r(cls,feats,class_sl,params['n_boots'],params['f_boots'],params['lda_abs_th'],0.0000000001,params['nlogs']) File "/export/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/lefse.py", line 199, in test_lda_r robjects.r('effect.size <- abs(mean(LD[sub_d[,"class"]=="'+p[0]+'"]) - mean(LD[sub_d[,"class"]=="'+p[1]+'"]))') File "/galaxy_venv/local/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 358, in __call__ p = _rparse(text=StrSexpVector((string,))) rpy2.rinterface.RRuntimeError: Error in (function (file = "", n = NULL, text = NULL, prompt = "?", keep.source = getOption("keep.source"), : <text>:1:47: unexpected numeric constant 1: effect.size <- abs(mean(LD[sub_d[,"class"]==""1 ^ For your reference, I am using this tool to analyze human gut microbiome data. Also, I cross-posted to the forum (link: https://help.galaxyproject.org/t/lda-effect-size-error/2840) Any guidance would be greatly appreciated. all the best, Caroline -- Caroline M. Kelsey Developmental Psychology Ph.D. Candidate UVA Babylab: http://uvababylab.org/ The University of Virginia

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