- galaxy-dev - lists.galaxyproject.org

Error running JBrowse
by Raymond Wan 16 Aug '16

16 Aug '16

Dear all, I'm trying to run the JBrowse tool within Galaxy. The installation was fine (I think), but when I run the tool, I get this error: Fatal error: Exit code 1 () Traceback (most recent call last): File "/d15/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/d022577ff9cf/jbrowse/jbrowse.py", line 11, in <module> from Bio.Data import CodonTable ImportError: No module named Does this mean I'm missing something? In the history, if I click the "(i)" icon for the incomplete job (in red), everything looks fine, except that it says: Tool Version: python: can't open file 'jbrowse.py': [Errno 2] No such file or directory However, "jbrowse.py" does exist in the path above. Any idea what could be wrong? Thank you! Ray

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Modifying a Cloud Cluster Instance
by Lapointe, David 11 Aug '16

11 Aug '16

I have a Cloudman instance up and running, but I would like to add SSL ( I have a signed cert and key ) and productionize it. I see several methods documented,but it's not clear which one is preferred: edit in place then persist changes and restart (wiki/Cloudman/CustomizeGalaxyCloud) seems best to me. Any advice? Thanks David -- David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144 Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

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Adding a download link to the "Download or Export Workflow" page with load balancing
by Alex Rodriguez 11 Aug '16

11 Aug '16

Dear Galaxy developers, I am interested in adding a download link to the “Download or Export Workflow” page of a workflow. I am able to add the link through the files in the templates directory and correctly add the necessary API functions in the lib/webapps/galaxy/controllers/workflow.py file. I wanted to ask for some help in figuring out what I might be missing when I try to download a file when I have load balancing feature activated. The page looks something like this: Download to File Download workflow to file so that it can be saved or imported into another Galaxy server. <https://dev.globusgenomics.org/u/arodri7/w/workflow-1-for-asms-2016-worksho…> New Test Download ( test file) URL for Importing to Another Galaxy This workflow must be accessible before it can be imported into another Galaxy. <https://dev.globusgenomics.org/workflow/sharing?id=a728237e0d32bb8c> As you can see I added the “New test Download” link. I have added and tested the function which gets me the information about the workflow I want correctly. For now it’s just a “hello world” string. When I don’t use load balancing I get the contents I want downloaded to the file correctly. However, when I activate load balancing, it only downloads an empty file. I can print the contents of the test download file to the galaxy log, but as I said nothing gets printed on the actual file. Is there some javascript code I also need to add for this functionality that I might be missing such that the download works with load balancing? As I mentioned I do get a proper download when load balancing is not activated. BTW, all other existing download links work properly with both load balancing and no load balancing. Thanks, Alex

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Travis CI for Galaxy repositories?
by Peter van Heusden 11 Aug '16

11 Aug '16

Hi everyone We maintain a tools collection on Github for tools that are not yet (or will never be) added to tools-iuc: https://github.com/SANBI-SA/tools-sanbi-uwc I tried copying the .travis.yml from tools-iuc to our repository, and it largely works, except for the planemo upload part, which fails with this error: Repository created cd '/home/pvh/Documents/code/SANBI/pilon/tools-sanbi-uwc/tools/pilon' && git rev-parse HEAD cd '/home/pvh/Documents/code/SANBI/pilon/tools-sanbi-uwc/tools/pilon' && git diff --quiet Could not update pilon Unexpected response from galaxy: 500: {"content_alert": "", "err_msg": "Metadata may have been defined for some items in revision 'f2477672a950'. Correct the following problems if necessary and reset metadata.<br/><b>pilon.xml<\/b> - This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct this error.<br/><br/>"} This is related to the pilon tool in that repo (tools/pilon). The tool in question optionally uses a dataset from all_fasta, I'm not sure if that is relevant for the error. BTW this error happened on push, not on PR. Any ideas? Thanks, Peter

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Doubled arguments from loc files in tests
by Peter Cock 10 Aug '16

10 Aug '16

Hello all, Recently I've been debugging various problems with my Galaxy tool TravisCI tests as part of moving to using "planemo test" rather than the fragile system I first created which mimicked a pre-ToolShed manual install: https://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galax… Progress: https://travis-ci.org/peterjc/galaxy_mira - passing now :) https://travis-ci.org/peterjc/pico_galaxy - probably a loc file problem https://travis-ci.org/peterjc/galaxy_blast - different loc file problem This email is about the problems testing the BLAST wrappers where I am using a BLAST database defined in test-data/*.loc files. (I wasted some time today trying moving/copying the loc files and databases to different places before I noticed the issue below) Problem lines quoted are from this run, galaxy master or dev branch: https://travis-ci.org/peterjc/galaxy_blast/builds/150072050 as of this commit: https://github.com/peterjc/galaxy_blast/commit/03f81e7fb1e0562b46b8b2a2079c… Some of the command expect a single BLAST database from the test-data/*.loc files, and the test should do that, but we get: blastdbcmd ... -db path,path ... rpsblast ... -db path,path ... rpstblastn ... -db path,path ... Here we should get ... -db path (once only), not repeated with a comma, e.g. galaxy.jobs.command_factory INFO 2016-08-05 14:55:08,543 Built script [/tmp/tmp9NURC9/job_working_directory/000/58/tool_script.sh] for tool command[blastdbcmd -version > /tmp/tmp9NURC9/tmp/GALAXY_VERSION_STRING_58 2>&1; blastdbcmd -dbtype prot -db "/home/travis/build/peterjc/galaxy_blast/test-data/four_human_proteins.fasta,/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test-data/four_human_proteins.fasta" -info -out "/tmp/tmp9NURC9/files/000/dataset_58.dat"] For other tools you can select multiple databases as input, and the blastn tests try that, e.g. a working test gave this (where the space is deliberate as that's how the NCBI handle multiple DB arguments): blastn ... -db "path1 path2" galaxy.jobs.command_factory INFO 2016-08-05 14:58:01,783 Built script [/tmp/tmp9NURC9/job_working_directory/000/76/tool_script.sh] for tool command[blastn -version > /tmp/tmp9NURC9/tmp/GALAXY_VERSION_STRING_76 2>&1; blastn -query "/tmp/tmp9NURC9/files/000/dataset_75.dat" -db "/home/travis/build/peterjc/galaxy_blast/test-data/three_human_mRNA.fasta /home/travis/build/peterjc/galaxy_blast/galaxy-dev/test-data/three_human_mRNA.fasta" -task megablast -evalue 0.001 -out "/tmp/tmp9NURC9/files/000/dataset_76.dat" -outfmt 6 -num_threads "${GALAXY_SLOTS:-8}"] But when a single database is given we get a repeated path: blastn ... -db "path path" galaxy.jobs.command_factory INFO 2016-08-05 14:58:22,901 Built script [/tmp/tmp9NURC9/job_working_directory/000/78/tool_script.sh] for tool command[blastn -version > /tmp/tmp9NURC9/tmp/GALAXY_VERSION_STRING_78 2>&1; blastn -query "/tmp/tmp9NURC9/files/000/dataset_77.dat" -db "/home/travis/build/peterjc/galaxy_blast/test-data/rhodopsin_nucs.fasta /home/travis/build/peterjc/galaxy_blast/galaxy-dev/test-data/rhodopsin_nucs.fasta" -task megablast -evalue 0.001 -out "/tmp/tmp9NURC9/files/000/dataset_78.dat" -outfmt 6 -num_threads "${GALAXY_SLOTS:-8}"] Any thoughts on where this is breaking? In planemo? These tests are working locally via "planemo test" (older version of planemo, older version of Galaxy, Python 2.6). Peter

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Connecting LDAP with Galaxy
by Yip, Miu ki 09 Aug '16

09 Aug '16

Hi, I’m trying to configure a new instance of Galaxy and I want to use LDAP for user authentication. I have taken a look at this wiki page: https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth I followed the instructions and when I looked into the auth_conf.xml file, I was unsure of what exactly Galaxy is looking for when trying to connect with LDAP. Are there specific options that I must give it? May I ask how Galaxy uses LDAP to authenticate users? Thank you, Miuki Yip

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view details not working
by Vincent Cahais 09 Aug '16

09 Aug '16

Dear all, I have a very strange bug on my galaxy server. The view details button is not working anymore for the new datasets. I get an Internal server Error. It's still working for older datasets, it's only an issue for the new one, independently of the tool. Best regards Vincent **.**.***.*** - - [08/août/2016:15:32:31 +0200] "GET /galaxy/datasets/38ebe14f4d38806a/show_params HTTP/1.1" 500 - "http://galaxy*******/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:48.0) Gecko/20100101 Firefox/48.0" Error - <type 'exceptions.UnicodeDecodeError'>: 'ascii' codec can't decode byte 0xc3 in position 10: ordinal not in range(128) URL: http://galaxy.iarc.fr/galaxy/datasets/38ebe14f4d38806a/show_params File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 151 in __call__ app_iter = self.application(environ, sr_checker) File '/home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 179 in __call__ return self.app( environ, start_response ) File '/home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 126 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in handle_request body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 1030 in show_params has_parameter_errors=has_parameter_errors ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 809 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 823 in fill_template_mako return template.render( **data ) File '/home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/template.py', line 445 in render return runtime._render(self, self.callable_, args, data) File '/home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/runtime.py', line 829 in _render **_kwargs_for_callable(callable_, data)) File '/home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/runtime.py', line 864 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/runtime.py', line 890 in _exec_template callable_(context, *args, **kwargs) File '/home/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', line 61 in render_body __M_writer(unicode(next.body())) File '/home/galaxy/galaxy-dist/database/compiled_templates/show_params.mako.py', line 74 in render_body __M_writer(unicode(hda.create_time.strftime(trans.app.config.pretty_datetime_format))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 10: ordinal not in range(128) CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5' HTTP_AUTHORIZATION: 'Basic Y2FoYWlzdjpXMXNtM3JoMWxs' HTTP_CONNECTION: 'close' HTTP_COOKIE: 'galaxysession=09218edcc0a8a75b31582a2cb50d757dc5f67b9b7cae48d9fdb3bd88e9d143d956083945f07b4710; galaxycommunitysession=aeaf4b69c51e3d6d293956655fa9014fb7b92937bf5c098a096ed54161b02239b63b34c44bba22ac; toolshedgalaxyurl="http://galaxy********/"; PPA_ID=56sqtkiu7jrubvee6tk03a3ve6; webfx-tree-cookie-persistence=wfxt-4+wfxt-6+wfxt-10+wfxt-16+wfxt-18+wfxt-20' HTTP_DNT: '1' HTTP_HOST: 'galaxy*****' HTTP_REFERER: 'http://galaxy*******/' HTTP_REMOTE_USER: '*********' HTTP_UPGRADE_INSECURE_REQUESTS: '1' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:48.0) Gecko/20100101 Firefox/48.0' PATH_INFO: '/datasets/38ebe14f4d38806a/show_params' REMOTE_ADDR: '10.10.13.120' REQUEST_METHOD: 'GET' SCRIPT_NAME: '/galaxy' SERVER_NAME: '***********' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x7f5c49747cd0> is_api_request: False paste.cookies: (<SimpleCookie: PPA_ID='56sqtkiu7jrubvee6tk03a3ve6' galaxycommunitysession='aeaf4b69c51e3d6d293956655fa9014fb7b92937bf5c098a096ed54161b02239b63b34c44bba22ac' galaxysession='09218edcc0a8a75b31582a2cb50d757dc5f67b9b7cae48d9fdb3bd88e9d143d956083945f07b4710' toolshedgalaxyurl='http://galaxy**************/' webfx-tree-cookie-persistence='wfxt-4+wfxt-6+wfxt-10+wfxt-16+wfxt-18+wfxt-20'>, 'galaxysession=09218edcc0a8a75b31582a2cb50d757dc5f67b9b7cae48d9fdb3bd88e9d143d956083945f07b4710; galaxycommunitysession=aeaf4b69c51e3d6d293956655fa9014fb7b92937bf5c098a096ed54161b02239b63b34c44bba22ac; toolshedgalaxyurl="http://galaxy********/"; PPA_ID=56sqtkiu7jrubvee6tk03a3ve6; webfx-tree-cookie-persistence=wfxt-4+wfxt-6+wfxt-10+wfxt-16+wfxt-18+wfxt-20') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x7f5c4015fb50> paste.httpserver.proxy.host: 'dummy' paste.httpserver.proxy.scheme: 'http' paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x7f5c5c1f1cd0> paste.recursive.forward: <paste.recursive.Forwarder from /galaxy> paste.recursive.include: <paste.recursive.Includer from /galaxy> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /galaxy> paste.recursive.script_name: '/galaxy' paste.throw_errors: True request_id: '8e983af65d6c11e6beadbc305bad8bf8' webob._parsed_query_vars: (GET([]), '') wsgi process: 'Multithreaded'

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External user auth and API
by Sarah DIEHL 08 Aug '16

08 Aug '16

Dear all, since no one replied so far to the main problem I had and it might have gotten lost in the conversation, I ask again: Does somebody know how to configure external user auth with apache such that API (from external, e.g. bioblend) and dataset import in the data libraries work? When I configure apache to require auth for everything, the API does not work. If I except the API from the apache auth, the dataset import does not work. If I switch to the new galaxy-internal LDAP auth features, will that solve this problem? Any hints are appreciated! Best regards, Sarah ---- Sarah Diehl HPC System Administrator UNIVERSITÉ DU LUXEMBOURG LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE Campus Belval | Biotech II 6, avenue du Swing L-4371 Belvaux T +352 46 66 44 5360 sarah.diehl(a)uni.lu<mailto:sarah.diehl@uni.lu> http://lcsb.uni.lu<http://lcsb.uni.lu/> ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. ----- From: galaxy-dev <galaxy-dev-bounces(a)lists.galaxyproject.org<mailto:galaxy-dev-bounces@lists.galaxyproject.org>> on behalf of Sarah DIEHL <sarah.diehl(a)uni.lu<mailto:sarah.diehl@uni.lu>> Date: Monday 1 August 2016 13:06 To: Nicola Soranzo <nsoranzo(a)tiscali.it<mailto:nsoranzo@tiscali.it>>, "galaxy-dev(a)lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>" <galaxy-dev(a)lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>> Subject: Re: [galaxy-dev] Remote user auth and API Hi Nicola, thanks a lot for the help! Yes, it's a self-signed certificate, I didn't bother with letsencrypt yet ;-). So now the error turned to ConnectionError: GET: error 401: b'<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">\n<html><head>\n<title>401 Authorization Required</title>\n</head><body>\n<h1>Authorization Required</h1>\n<p>This server could not verify that you\nare authorized to access the document\nrequested. Either you supplied the wrong\ncredentials (e.g., bad password), or your\nbrowser doesn\'t understand how to supply\nthe credentials required.</p>\n</body></html>\n', 0 attempts left: None which is what I expected, since apache now wants the authentication through LDAP. So anybody know what the right settings are to get both the dataset import and the API working with external user auth over apache and LDAP? Thanks, Sarah ---- Sarah Diehl HPC System Administrator UNIVERSITÉ DU LUXEMBOURG LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE Campus Belval | Biotech II 6, avenue du Swing L-4371 Belvaux T +352 46 66 44 5360 sarah.diehl(a)uni.lu<mailto:sarah.diehl@uni.lu> http://lcsb.uni.lu<http://lcsb.uni.lu/> ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. ----- From: Nicola Soranzo <nicola.soranzo(a)gmail.com<mailto:nicola.soranzo@gmail.com>> on behalf of Nicola Soranzo <nsoranzo(a)tiscali.it<mailto:nsoranzo@tiscali.it>> Date: Monday 1 August 2016 12:58 To: Sarah DIEHL <sarah.diehl(a)uni.lu<mailto:sarah.diehl@uni.lu>>, "galaxy-dev(a)lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>" <galaxy-dev(a)lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>> Subject: Re: [galaxy-dev] Remote user auth and API Hi Sarah! I guess that your problem is with an untrusted certificate, you can get one for free at https://letsencrypt.org/ You can disable certificate verification in bioblend as in the example below: import bioblend.galaxy gi = bioblend.galaxy.GalaxyInstance(url=my_server, key=my_key) gi.verify = False Cheers, Nicola On 01/08/16 09:08, Sarah DIEHL wrote: Dear all, since the recent update to 16.04 I get the following error when trying to import a file from a user directory to a data library: AssertionError: use_remote_user is set but HTTP_REMOTE_USER header was not provided I use apache as a proxy and use an LDAP server for authentication. In order to get the API to work previously the apache had to be set to not check authentication for the requests to /api. In the logs I can see that the dataset import is an request to the API, so since the auth is not checked then, there is also no REMOTE_USER header set. What is the recommended way to solve this issue with the current Galaxy version? I disabled the special settings for /api and the dataset import works now. I tried to check the API with an old test script based on bioblend, but I now get the following error: ConnectionError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:645), 0 attempts left: None Previously I could disable it with import requests requests.packages.urllib3.disable_warnings() but that doesn't seem to work anymore (switched to Python 3 now). Since bioblend wraps all the requests methods, I cannot apply any of the common solutions I found online (e.g. set verify=False). Any help to solve these issues is highly appreciated :-). Best regards, Sarah ---- Sarah Diehl HPC System Administrator UNIVERSITÉ DU LUXEMBOURG LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE Campus Belval | Biotech II 6, avenue du Swing L-4371 Belvaux T +352 46 66 44 5360 <mailto:sarah.diehl@uni.lu>sarah.diehl(a)uni.lu<mailto:sarah.diehl@uni.lu> http://lcsb.uni.lu<http://lcsb.uni.lu/> ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. ----- ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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Adding packages to depot.galaxyproject.org
by Peter Cock 08 Aug '16

08 Aug '16

Hello all, How do tool wrapper developers/packagers go about adding entries to the Galaxy depot? There isn't a GitHub repository for this is there? Specifically I want to upload some older MIRA releases, e.g. these URLs have broken, but I have the original files and checksums: http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mi… http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mi… See also: https://www.freelists.org/post/mira_talk/Stable-download-URLs-on-sourceforge https://www.freelists.org/post/mira_talk/MIRA-495-now-missing-on-SourceForge I'm now running "planemo lint --urls ..." under TravisCI which flags the broken URLs immediately (rather than finding out when the installation fails later): https://github.com/peterjc/galaxy_mira/commit/4e26a4e3f3d69adaab657cb614e56… https://travis-ci.org/peterjc/galaxy_mira/jobs/150025836 Regards, Peter

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pop up on click
by Mohamed Kassam 08 Aug '16

08 Aug '16

Dear all, I have create a tool on javascript and html. I tried to use the xml tool from ucsc and flymine. I would like to know if it is possible to replace <inputs action="http://www.flymine.org" check_values="false" method="get"> <display>go to Flymine server $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" /> </inputs> By something like onclick it will display a pop up windows instead of opening the html adress on the same window. Best regards, Mohamed

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