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

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 *

3 4

[GSoC 2020] [Open Genome Informatics] Google Summer of Code 2020 Participation
by Robin Haw 28 Jan '20

28 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.

1 0

[GSoC 2020] [Open Genome Informatics] Google Summer of Code 2020 Participation
by Robin Haw 28 Jan '20

28 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.

1 0

LDA Effect Size (LEfSE) error
by Caroline Kelsey 23 Jan '20

23 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

1 0

Unable to install dwgsim from toolshed
by Peter Briggs 20 Jan '20

20 Jan '20

Hello all I'm experiencing an issue trying to install the 'dwgsim' from the toolshed: https://toolshed.g2.bx.psu.edu/view/nilshomer/dwgsim/512671604bab I've tried installing into a couple of production instances (both running 19.05) as well as local instances running 19.05 and 19.09, but all attempts have failed. Installing other tools e.g. FastQC seems to work ok. From the log for the 19.09 local instance I'm seeing the following error: tool_shed.galaxy_install.install_manager ERROR 2020-01-20 14:36:19,721 [p:2159,w:1,m:0] [uWSGIWorker1Core3] Error attempting to retrieve installation information from tool shed https://toolshed.g2.bx.psu.edu/ for revision 512671604bab of repository dwgsim owned by nilshomer Traceback (most recent call last): File "lib/tool_shed/galaxy_install/install_manager.py", line 461, in __get_install_info_from_tool_shed raw_text = util.url_get(tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params) File "lib/galaxy/util/__init__.py", line 1677, in url_get response = urlopener.open(full_url) File "XXX/python/2.7.10/lib/python2.7/urllib2.py", line 437, in open response = meth(req, response) File "XXX/python/2.7.10/lib/python2.7/urllib2.py", line 550, in http_response 'http', request, response, code, msg, hdrs) File "XXX/apps/python/2.7.10/lib/python2.7/urllib2.py", line 475, in error return self._call_chain(*args) File "XXX/apps/python/2.7.10/lib/python2.7/urllib2.py", line 409, in _call_chain result = func(*args) File "XXX/apps/python/2.7.10/lib/python2.7/urllib2.py", line 558, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error Is there something special about this tool which means it can't be installed from the tool shed? Any help is appreciated Best wishes Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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January Galaxy News: BCC2020, PAG & ABRF; New pubs, platforms, tutorials...
by Dave Clements 08 Jan '20

08 Jan '20

Hello all, The January 2020 Galactic News is out! https://galaxyproject.org/news/2020-01-galaxy-update/ - 13 Upcoming Events - BCC2020 training topic nominations, Register for Galaxy Admin Training, Galaxy @ PAG & ABRF, and training @ Earlham and Rennes. - 172 new publications - Six highlighted pubs from RT-qPCR to functional genomics - Two new blog posts - PGP-UK and Crowdsourcing Science - Galaxy Platform News - Three new platforms, UseGalaxy.* news, and platforms in pubs - Training material and doc updates - R, RStudio, ATAC-Seq, Scanpy, and Single Cell RNA-Seq - And other news too If you have anything to include to next month's newsletter, then please send it to outreach(a)galaxyproject.org. And a happy new year too, :-) Dave C on behalf of the Galaxy community -- https://galaxyproject.org/

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