July 2019 - galaxy-dev - lists.galaxyproject.org

Still problems running ML tools from toolshed
by Nancy Ide 17 Jul '19

17 Jul '19

Running the ml_performance_plots tool I get this error: Fatal error: Exit code 1 () Traceback (most recent call last): File "/Users/ide/Projects/GitHub/GalaxyMods/tools/learning/ml_performance.py", line 156, in <module> main(args.infile_input, args.infile_output, args.infile_trained_model) File "/Users/ide/Projects/GitHub/GalaxyMods/tools/learning/ml_performance.py", line 83, in main model = pickle.load(model_file) File "/usr/local/Cellar/python@2/2.7.16/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.py", line 1384, in load return Unpickler(file).load() File "/usr/local/Cellar/python@2/2.7.16/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.py", line 864, in load dispatch[key](self) File "/usr/local/Cellar/python@2/2.7.16/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.py", line 892, in load_proto raise ValueError, "unsupported pickle protocol: %d" % proto ValueError: unsupported pickle protocol: 3 Please help! ----------------------------------------------------- Nancy Ide Professor of Computer Science Department of Computer Science Vassar College Poughkeepsie, New York 12604-0520 USA tel: (+1 845) 437 5988 fax: (+1 845) 437 7498 email: ide(a)cs.vassar.edu http://www.cs.vassar.edu/~ide -----------------------------------------------------

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Re: Bismark - Bug in Bismark Pretty Report ?
by Previti 15 Jul '19

15 Jul '19

Dear Björn, This works now...but I don't know why... Maybe a combination of a Galaxy update and correctly whitelisting the tool for displaying html output.... Thanks for getting back to me! Christopher On 7/13/19 1:45 PM, Björn Grüning wrote: > Uha, this looks like a upstream bug, not sure how this can be Galaxy > related. > > Is this still a problem? > > Cheers, > Bjoern > > Am 08.03.19 um 09:23 schrieb Previti: >> Dear Galaxy Community, >> >> I just recently started testing the Bismark methylation tools, >> everything works fine until I try to make a "pretty report". >> Some information is not included in the report, instead you see >> placeholders >> I attached the output I get and shown below are the job parameters. >> Does anybody know where to fix this? >> >> Best regards, >> Christopher >> >> >> Bismark Pretty Report >> >> >> Dataset Information >> >> Number: 198 >> Name: Bismark Pretty Report on data 190, data 189, and others: >> Download pretty html report >> Created: Thu 07 Mar 2019 03:24:40 PM (UTC) >> Filesize: 2.7 MB >> Dbkey: ? >> Format: html >> >> >> Job Information >> >> Galaxy Tool ID: >> toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_pretty_report/0.20.0 >> Galaxy Tool Version: 0.20.0 >> Tool Version: >> Tool Standard Output: stdout >> <http://dkfzgalaxy/datasets/971c2f882eb14ac3/stdout> >> Tool Standard Error: stderr >> <http://dkfzgalaxy/datasets/971c2f882eb14ac3/stderr> >> Tool Exit Code: 0 >> History Content API ID: 971c2f882eb14ac3 (41433) >> Job API ID: 58816697357e736f (22051) >> History API ID: 5fccce9c1b3793da (807) >> UUID: 45bedd12-6ce5-4d63-a1e2-e05883b0c356 >> Full Path: /opt/galaxy/galaxy/database/files/038/dataset_38737.dat >> >> >> Tool Parameters >> >> Input Parameter Value Note for rerun >> Submit a Bismark mapping report 191: Bismark Meth. Extractor on >> data 60 and data 133: Genome-wide methylation report. >> <http://dkfzgalaxy/datasets/c53067deacfc4f28/show_params> >> additional_reports >> Submit the corresponding Bismark deduplication report 197: >> Bismark Deduplicate on data 133: deduplication report >> <http://dkfzgalaxy/datasets/622377f5e70addd2/show_params> >> Submit the corresponding Bismark splitting report 189: Bismark >> Meth. Extractor on data 60 and data 133: Splitting Report >> <http://dkfzgalaxy/datasets/aa40ffd063a4645f/show_params> >> Submit the corresponding Bismark M-bias report 190: Bismark Meth. >> Extractor on data 60 and data 133: Mbias Report >> <http://dkfzgalaxy/datasets/47db6b20871008b9/show_params> >> Submit the corresponding Bismark nucleotide report >> >> Create a separate logfile, otherwise logs are added to the dataset >> info. False >> >> >> Inheritance Chain >> >> Bismark Pretty Report on data 190, data 189, and others: Download >> pretty html report >> >> >> Command Line >> >> python >> '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/bismark/7bffcb6fc81d/bismark/bismark2report_wrapper.py' >> --alignment_report >> '/opt/galaxy/galaxy/database/files/038/dataset_38715.dat' >> --dedup_report >> '/opt/galaxy/galaxy/database/files/038/dataset_38736.dat' >> --splitting_report >> '/opt/galaxy/galaxy/database/files/038/dataset_38713.dat' >> --mbias_report >> '/opt/galaxy/galaxy/database/files/038/dataset_38714.dat' >> --output_html_report >> '/opt/galaxy/galaxy/database/files/038/dataset_38737.dat' >> >> >> Job Metrics >> >> >> core >> >> Cores Allocated 8 >> Job End Time 2019-03-07 16:49:58 >> Job Runtime (Wall Clock) 25 minutes >> Job Start Time 2019-03-07 16:24:43 >> Memory Allocated (MB) 510000 >> >> >> Job Dependencies >> >> Dependency Dependency Type Version >> bismark conda 0.20.0 >> >> >> >> -- >> *Dr. Christopher Previti* >> Genomics and Proteomics Core Facility >> High Throughput Sequencing (W190) >> Bioinformatician >> >> German Cancer Research Center (DKFZ) >> Foundation under Public Law >> Im Neuenheimer Feld 580 >> 69120 Heidelberg >> Germany >> Room: B2.102 (INF580/TP3) >> Phone: +49 6221 42-4661 >> >> christopher.previti(a)dkfz.de <http://www.dkfz.de/> >> www.dkfz.de <http://www.dkfz.de/> >> >> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta >> VAT-ID No.: DE143293537 >> >> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die >> Personen bestimmt, an die sie adressiert ist. >> Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte >> Informationen enthalten. Sollten Sie nicht >> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den >> Absender und löschen Sie die Mitteilung. >> Jegliche unbefugte Verwendung der Informationen in dieser Nachricht >> ist untersagt. >> >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> %(web_page_url)s >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/ >> -- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661 christopher.previti(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist. Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung. Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.

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How to resolve the dependency of self-compiled C++ programs when publishing a tool?
by Jin Li 11 Jul '19

11 Jul '19

Hi all, I want to publish our own tool to the Galaxy Tool Shed. Our tool is our own developed C++ program. Our compiled binaries may not necessarily run in other machines due to different OS platforms. How could I resolve the tool dependency of our own compiled binaries? Thank you. Best regards, Jin

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Error during tool installation: "inotify instance limit reached"
by Previti 10 Jul '19

10 Jul '19

Dear all, I've been getting this error for a few days now, it basically prevents anything from being installed on the first go. Individual tools can be installed, but even then I have to try multiple times. Any ideas how to fix this? Cheers, Christopher The details from galaxy.log are (installing an older VCFtools package): 172.22.24.119 - - [10/Jul/2019:10:44:32 +0200] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - "http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare_for_instal… set_revisions=34a6b690e4b5&repository_ids=2ba42187f2588c4b&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:67.0) Gecko/20100101 Firefox/67.0" galaxy.tools.toolbox.base DEBUG 2019-07-10 10:44:55,592 Appending to tool panel section: NGS:VCFtools 172.22.24.119 - - [10/Jul/2019:10:44:58 +0200] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare _for_install" "Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:67.0) Gecko/20100101 Firefox/67.0" 172.22.24.119 - - [10/Jul/2019:10:45:01 +0200] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare _for_install" "Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:67.0) Gecko/20100101 Firefox/67.0" 172.22.24.119 - - [10/Jul/2019:10:44:55 +0200] "POST /admin_toolshed/install_repositories HTTP/1.1" 500 - "http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare_for_install" "Moz illa/5.0 (X11; Fedora; Linux x86_64; rv:67.0) Gecko/20100101 Firefox/67.0" *Error - <type 'exceptions.OSError'>: inotify instance limit reached* URL: http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/install_repositori… File '/opt/galaxy/galaxy/lib/galaxy/web/framework/middleware/error.py', line 154 in __call__ app_iter = self.application(environ, sr_checker) File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/opt/galaxy/galaxy/lib/galaxy/web/framework/base.py', line 143 in __call__ return self.handle_request(environ, start_response) File '/opt/galaxy/galaxy/lib/galaxy/web/framework/base.py', line 222 in handle_request body = method(trans, **kwargs) File '/opt/galaxy/galaxy/lib/galaxy/web/framework/decorators.py', line 101 in decorator return func(self, trans, *args, **kwargs) File '/opt/galaxy/galaxy/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 575 in install_repositories reinstalling=reinstalling, File '/opt/galaxy/galaxy/lib/tool_shed/galaxy_install/install_manager.py', line 846 in install_repositories tool_panel_section_mapping=tool_panel_section_mapping) File '/opt/galaxy/galaxy/lib/tool_shed/galaxy_install/install_manager.py', line 893 in install_tool_shed_repository tool_panel_section_mapping=tool_panel_section_mapping) File '/opt/galaxy/galaxy/lib/tool_shed/galaxy_install/install_manager.py', line 544 in __handle_repository_contents repository_tools_tups = irmm.get_repository_tools_tups() File '/opt/galaxy/galaxy/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py', line 75 in get_repository_tools_tups tool = self.app.toolbox.load_tool(os.path.abspath(load_relative_path), guid=guid, use_cached=False) File '/opt/galaxy/galaxy/lib/galaxy/tools/toolbox/base.py', line 766 in load_tool self.watch_tool(tool) File '/opt/galaxy/galaxy/lib/galaxy/tools/toolbox/base.py', line 774 in watch_tool self._tool_watcher.watch_file(tool.config_file, tool.id) File '/opt/galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py', line 198 in watch_file self.monitor(tool_dir) File '/opt/galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py', line 190 in monitor self.observer.schedule(self.event_handler, dir, recursive=False) File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py', line 293 in schedule emitter.start() File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/watchdog/utils/__init__.py', line 110 in start self.on_thread_start() File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/inotify.py', line 121 in on_thread_start self._inotify = InotifyBuffer(path, self.watch.is_recursive) File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/inotify_buffer.py', line 35 in __init__ self._inotify = Inotify(path, recursive) File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/inotify_c.py', line 188 in __init__ Inotify._raise_error() *File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/inotify_c.py', line 415 in _raise_error** ** raise OSError("inotify instance limit reached")** **OSError: inotify instance limit reached** * CGI Variables ------------- CONTENT_LENGTH: '12169' CONTENT_TYPE: 'application/x-www-form-urlencoded; charset=UTF-8' HTTP_ACCEPT: 'text/html, */*; q=0.01' HTTP_ACCEPT_ENCODING: 'gzip,deflate' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a9d01bef828912a83dd6a820b8a47ad278d223920b71ba8b43726aaf1140b008e' HTTP_HOST: 'dkfzgalaxy.inet.dkfz-heidelberg.de' HTTP_REFERER: 'http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare_for_install' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:67.0) Gecko/20100101 Firefox/67.0' HTTP_X_FORWARDED_FOR: '172.22.24.119' HTTP_X_FORWARDED_HOST: 'dkfzgalaxy.inet.dkfz-heidelberg.de' HTTP_X_FORWARDED_SERVER: 'fe80::216:3eff:fe80:c02b' HTTP_X_REQUESTED_WITH: 'XMLHttpRequest' ORGINAL_HTTP_HOST: 'localhost:8080' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/admin_toolshed/install_repositories' REMOTE_ADDR: '172.22.24.119' REQUEST_METHOD: 'POST' SERVER_NAME: '127.0.0.1' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x7f9f48207410> controller_action_key: u'web.admin_toolshed.install_repositories' is_api_request: False paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a9d01bef828912a83dd6a820b8a47ad278d223920b71ba8b43726aaf1140b008e'>, 'galaxysession=c6ca0ddb55be603a9d01bef828912a83dd6a820b8a47ad278d223920b71ba8b43726aaf1140b008e') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x7f9f48c86fd0> paste.httpserver.proxy.host: 'dummy' paste.httpserver.proxy.scheme: 'http' paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x7f9f486fcd90> paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: 'fd8cc98ea2ee11e9a89100163e80c02b' webob._body_file: (<_io.BufferedReader>, <socket._fileobject object at 0x7f9f3a4b5ad0 length=12169>) webob._parsed_post_vars: (MultiDict([('tool_shed_repository_ids', u"[u'ac218635d795e337', u'e3e09dfaa8fad8c8', u'1efe9eb0bff40152', u'358d8704ef89cb6b', u'cbc5119f47881258']"), ('encoded_kwd', u'59b03a7799b953da9827424b9cef2236c5b9f461: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... 0x7f9f35cdfed0>) webob._parsed_query_vars: (GET([]), '') webob.is_body_seekable: True wsgi process: 'Multithreaded' wsgi.input_terminated: True -- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661 christopher.previti(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist. Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung. Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.

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Error
by Nancy Ide 07 Jul '19

07 Jul '19

I get this error when trying to run "Plot confusion matrix, precision, recall and ROC and AUC curves": > CondaError: CondaHTTPError: HTTP 404 NOT FOUND for url <https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-7.3.0-hdf63c60_0.… <https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-7.3.0-hdf63c60_0.…>> as the file libgcc-ng-7.3.0-hdf63c60_0.tar.bz2 does not exist in https://conda.anaconda.org/conda-forge/linux-64/ <https://conda.anaconda.org/conda-forge/linux-64/> Please help! Thanks ----------------------------------------------------- Nancy Ide Professor of Computer Science Department of Computer Science Vassar College Poughkeepsie, New York 12604-0520 USA tel: (+1 845) 437 5988 fax: (+1 845) 437 7498 email: ide(a)cs.vassar.edu http://www.cs.vassar.edu/~ide -----------------------------------------------------

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Report an error
by Fernanda Manaia Demarqui 03 Jul '19

03 Jul '19

(33, "HTTP server doesn't seem to support byte ranges. Cannot resume.") Thanks, Fernanda

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