October 2014 - galaxy-dev - lists.galaxyproject.org

ToolShed tool preview broken (TestToolShed too)
by Peter Cock 08 Oct '14

08 Oct '14

Hi all, >From the "new tools" information Dave Compiled for the last Galaxy Update https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contributions I had a look at galaxyp's "filter_by_fasta_ids: Extract sequences from a FASTA file based on a list of IDs" tool: https://toolshed.g2.bx.psu.edu/view/galaxyp/filter_by_fasta_ids I wanted to see how it compared to my own similar tools (which handle FASTA, FASTQ, SFF and could cover more - they replaced my older single format filter tools): https://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id https://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id Now for the bug report, clicking on the button (under valid tools) which would normally give a preview of the tool form is failing - giving just "Internal Server Error". I have tried a random selection of other tools and this seems to be universal - moreover the TestToolShed also seems to have the same problem. Regards, Peter

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testtoolshed internal server error
by Stef van Lieshout 08 Oct '14

08 Oct '14

Anyone else getting this when trying to upload to a testtoolshed repos? I'm using the "upload files to repository" function in "repository actions" and get a blank page with "internal server error".. Worked fine yesterday. Ciao, Stef

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Internal Server Error on metadata reset
by Saket Choudhary 08 Oct '14

08 Oct '14

I am trying to reset metadata on all my repositories at once using the "Reset metadata on my repositories" button on https://testtoolshed.g2.bx.psu.edu/ It fails with: Internal Server Error Galaxy was unable to successfully complete your request URL: http://testtoolshed.g2.bx.psu.edu/repository/reset_metadata_on_my_writable_… Module galaxy.web.framework.middleware.error:149 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ >> environ, self.app) Module paste.wsgilib:543 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request >> body = method( trans, **kwargs ) Module galaxy.webapps.tool_shed.controllers.repository:2795 inreset_metadata_on_my_writable_repositories_in_tool_shed >> my_writable=True ) Module tool_shed.metadata.repository_metadata_manager:65 in build_repository_ids_select_field >> query = self.get_query_for_setting_metadata_on_repositories( my_writable=my_writable,order=True ) Module tool_shed.metadata.repository_metadata_manager:513 in get_query_for_setting_metadata_on_repositories >> .filter( or_( *clause_list ) ) NameError: global name 'or_' is not defined extra data

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Cloudman indices installation/configuration
by Iry Witham 08 Oct '14

08 Oct '14

Hi Team, I have a new instance of galaxy cloudman running and have added tools from the toolshed to it. When I attempt to run tools like sam-to-bam or any gatk tool I am prompted for a reference genome. However, indices/references not available for these tools. I have added the following line to the sam_fa_indices.loc, but that did nothing: index hg19 /mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/gh19.fa I have also added the following three lines to the gatk2_picard_index.loc: hg19 hg19 Human (hg19) /mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa GRCh37 GRCh37 Human (GRCh37) /mnt/galaxyIndices/genomes/Hsapiens/GRCh37/seq/GRCh37.fa mm10 mm10 Mouse (mm10) /mnt/galaxyIndices/genomes/Mmusculus/mm10/seq/mm10.fa I know I have missed something, but can't seem to figure it out. Could someone point me in the right direction? Regards, __________________________________ Iry T. Witham Scientific Applications Administrator Computational Sciences Group The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham(a)jax.org [cid:A4FA2ADE-F7C3-4B38-851C-6FE20C32198B] The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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clustalomega from toolshed installation issue
by Isabelle Phan 07 Oct '14

07 Oct '14

Hello, I installed clustalomega from the galaxy main toolshed using the admin interface of our local galaxy install. When I run the tool, I get this message: Dataset generation errors Dataset 55: co_alignment.fasta Tool execution generated the following error message: Error invoking command: clustalo --force --threads=1 --maxnumseq=300000 --maxseqlen=15000 -o /opt/galaxy-dist/database/files/000/dataset_158.dat -l /opt/galaxy-dist/database/files/000/dataset_159.dat -v -i /opt/galaxy-dist/database/files/000/dataset_153.dat [Errno 2] No such file or directory I've tried reloading my input file, reloading the tool's configuration, resetting the metadata on the clustalomega repository, deleting the tool completely and re-installing. No luck. If I try to rerun the job again, I get non-sensical errors that seem to originate from other tools, as if the database was completely garbled. Each of those tools work fine. Only clustalomega behaves oddly. I have no access to our galaxy server, so any solution would have to be implemented from the admin interface. thanks for any hints, Isabelle

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Apache proxy, SSL, and UCSC get data
by Lance Parsons 07 Oct '14

07 Oct '14

I'm having trouble after setting up SSL on our Apache proxy for Galaxy. When I try to import data from UCSC, Galaxy tries to go to the http (non-ssl) url for UCSC and thus generates a security error in the browser and the request is blocked. I have added RequestHeader set X-URL-SCHEME https to the httpd.conf and that appears to be working. Is there something else I need to do? Should I patch the data_source tools to use https in the xml tool definitions? Thanks for any advice. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Central tool shed installations fail due to redirect
by Kandalaft, Iyad 07 Oct '14

07 Oct '14

Hi Everyone I was recently trying to update tools that I installed from the central tool shed. However, it seems that a temporary redirect on the central tool shed server is causing my galaxy installation to throw a stack trace. Anyone else encountered this? Thanks in advance. URL: http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang… Module galaxy.web.framework.middleware.error:149 in __call__ >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> app_iter = self.application(environ, sr_checker) Module paste.lint:170 in lint_app >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> iterator = application(environ, start_response_wrapper) Module paste.recursive:84 in __call__ >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:92 in __call__ >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> return self.app( environ, start_response ) Module paste.httpexceptions:633 in __call__ >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> body = method( trans, **kwargs ) Module galaxy.web.framework:377 in decorator >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:1926 in update_to_changeset_revision >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> return self.prepare_for_install( trans, **new_kwd ) Module galaxy.web.framework:377 in decorator >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:1122 in prepare_for_install >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> updating=updating ) Module tool_shed.util.common_install_util:110 in get_dependencies_for_repository >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) ) Module tool_shed.util.common_install_util:451 in get_required_repo_info_dicts >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> response = urllib2.urlopen( request ).read() Module urllib2:126 in urlopen >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> return _opener.open(url, data, timeout) Module urllib2:397 in open >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> response = meth(req, response) Module urllib2:510 in http_response >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> 'http', request, response, code, msg, hdrs) Module urllib2:429 in error >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> result = self._call_chain(*args) Module urllib2:369 in _call_chain >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> result = func(*args) Module urllib2:595 in http_error_302 >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> new = self.redirect_request(req, fp, code, msg, headers, newurl) Module urllib2:556 in redirect_request >> <http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_chang…> raise HTTPError(req.get_full_url(), code, msg, headers, fp) HTTPError: HTTP Error 307: Temporary Redirect Iyad Kandalaft Bioinformatics Programmer Microbial Biodiversity Bioinformatics Science & Technology Branch Agriculture & Agri-Food Canada Iyad.Kandalaft(a)agr.gc.ca | (613) 759-1228

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installing R bioconductor package DNAcopy gfortran setup_r_environment
by Stef van Lieshout 07 Oct '14

07 Oct '14

Hi all, I'm trying to install R/bioconductor packages in galaxy and have trouble with some of them. I made a dependency package ("package_qdnaseq_1_0_5" in the testtoolshed) that should install several R (bioconductor) packages using "setup_r_environment" and for each package the <package>http://link/to/package.tar.gz</package> structure. It works for many but fails for the package "DNAcopy" with the error below complaining about gfortran, but that seems to be installed on my systems (tested two of them, ubuntu 12.04). When I install this with "install.packages" in my default R installation it installs without problems.. Anyway know how to deal with or debug this? Thanks, Stef ----- install_environment.STDOUT DEBUG 2014-10-07 14:04:13,176 Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/stef/BASE/tools/galaxy/galaxy-dist/tool-dependency/qdnaseq/1.0.5/stef/package_qdnaseq_1_0_5/42096296e06f/DNAcopy/libs/DNAcopy.so': /home/stef/BASE/tools/galaxy/galaxy-dist/tool-dependency/qdnaseq/1.0.5/stef/package_qdnaseq_1_0_5/42096296e06f/DNAcopy/libs/DNAcopy.so: undefined symbol: _gfortran_os_error Error: loading failed Execution halted Error in dyn.load(file, DLLpath = DLLpath, ...) : ERROR: loading failed * removing ‘/home/stef/BASE/tools/galaxy/galaxy-dist/tool-dependency/qdnaseq/1.0.5/stef/package_qdnaseq_1_0_5/42096296e06f/DNAcopy’

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CfP: Reproducible Science Hackathon - Curriculum & Workflow Development
by Tracy Teal 06 Oct '14

06 Oct '14

It would be great to have someone from the Galaxy community involved in this reproducible science hack-a-thon, as Galaxy is such a positive contribution to workflows in reproducible science. ================================== Reproducible Science Hackathon: Curriculum & Workflow Development ================================== Goal: Develop a short course curriculum for tools, resources, and practices for reproducible science. Location: NESCent, Durham, NC Dates and times: December 8 - 11, 2014; 9 am - 5pm each day To apply: http://goo.gl/GzS118 ; deadline October 10, 2014. Successful applicants will be notified by October 17th. Synopsis Making science more reproducible has enormous potential to accelerate scientific advance, including for practicing individuals. Despite this, the tools and approaches that are already available are rarely taught. To address this, we are organizing a 4-day workshop aimed at developing, and later teaching, a short course curriculum for tools, resources, and practices for reproducible science. A part of the workshop will also be devoted to addressing gaps that hinder the broad adoption of such resources. The event will be held December 8-11,2014, in Durham, NC, at the National Evolutionary Synthesis Center (NESCent). We aim to assemble a diverse and interdisciplinary group of participants, and invite those interested to apply by Oct 10 at http://goo.gl/GzS118. The full Call for Participation can be found here: http://goo.gl/IzACr3

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Get Data - url upload (connection timed out)
by Elizabeth Chia 03 Oct '14

03 Oct '14

Dear * I have a local galaxy instance installed on a cluster. I've been trying to upload data by URL but kept getting this error: *"unable to fetch <url of data> [Errno socket error] [Errno 110] connection timed out". *I've tried with and without file compression format and still gives me that error. Am I suppose to modify/edit any particular config file? Can't seem to find a similar thread or answer to this but perhaps I may have missed. Apologies if I have missed. Would appreciate if anyone can please advise. Thanks. Best regards liz

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