galaxy-dev August 2014

galaxy-dev@lists.galaxyproject.org

65 participants
102 discussions

ssl proxy
by Shrum, Donald C 26 Aug '14

26 Aug '14

Hi all, I have a galaxy install with an apache proxy and ldap authentication. <Location /> RequestHeader set X-URL-SCHEME https AuthBasicProvider ldap Other stuff.... </Location> RewriteEngine on RewriteRule ^/static/style/(.*) /panfs/storage.local/opt/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /panfs/storage.local/opt/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /panfs/storage.local/opt/galaxy-dist/static/$1 [L] RewriteRule ^/favicon.ico /panfs/storage.local/opt/galaxy-dist/static/favicon.ico [L] RewriteRule ^/robots.txt /panfs/storage.local/opt/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://144.174.51.187:8080$1 [P] What is the best way to manage the redirect from http to https for the authentication?

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How to build an application that uses a set of files?
by George Weingart 23 Aug '14

23 Aug '14

Hello, I would like to get advice how to implement the following application into Galaxy: We have a set of say, 17 tabular files, we would like to present them to the User and allow him to select a subset of them, say 9. Once he selected these files we would like to invoke our program “merge.py” against the subset of 9 files the User selected whose result is an output of one file. How would the xml look? Thanks! George Weingart

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Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY
by Peter Cock 22 Aug '14

22 Aug '14

On Fri, Aug 22, 2014 at 8:18 PM, Marija Atanaskovic <matan(a)unimelb.edu.au> wrote: > Hi Peter, > > I don¹t know what the stdout and stderr information was. I click on it but > nothing comes up. > > I installed from the main toolshed: > http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler > Yes, I did use the test toolshed for Mira 4. > > Regards, > > Marija If stdout and stderr are empty, this is consistent with MIRA never even starting (as suggested by the next bit of information below). On Fri, Aug 22, 2014 at 8:20 PM, Marija Atanaskovic <matan(a)unimelb.edu.au> wrote: > Hi Peter, > > This is the error in history under MIRA log: > > tool error > An error occurred with this dataset:Unable to run job due to a > misconfiguration of the Galaxy job running system. Please contact a site > administrator. > > Regards, > > Marija That suggests your Galaxy job runner is not properly configured, and MIRA itself was never started. Are you the site administrator? Are other Galaxy tools working? Are other Galaxy tools installed from the ToolShed working? On Fri, Aug 22, 2014 at 8:22 PM, Marija Atanaskovic <matan(a)unimelb.edu.au> wrote: > Hi Peter, > > One more thing. The data that I am trying to analyse are fastq files of > Ion Torrent reads. I have used them with other assemblers e.g., velvet, > CLC. > > Marija I have not personally used Ion Torrent, but that ought to be fine. Peter P.S. You forgot to CC the mailing list.

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Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY
by Marija Atanaskovic 22 Aug '14

22 Aug '14

Mira doesn’t work on Galaxy. This is the log message I receive. Tool: Assemble with MIRA v3.4 Name: MIRA log Created: Fri Aug 22 00:24:38 2014 (UTC) Filesize: 0 bytes Dbkey: ? Format: txt Galaxy Tool Version: 0.0.10 Tool Version: None Tool Standard Output: stdout<http://130.56.251.91/datasets/d5f55b83db1f410a/stdout> Tool Standard Error: stderr<http://130.56.251.91/datasets/d5f55b83db1f410a/stderr> Tool Exit Code: None API ID: d5f55b83db1f410a Full Path: /mnt/galaxy/files/000/dataset_326.dat Input Parameter Value Note for rerun Assembly method De novo Assembly type Genome Assembly quality grade Accurate Backbones/reference chromosomes? false Sanger/Capillary reads? false 454 reads? false Solexa/Illumina reads? false Ion Torrent reads? true Ion Torrent reads file 10: R_2011_10_19_14_30_56_user_SN1-36_Auto_SN1-36_38.fastq Inheritance Chain MIRA log Also I can’t install Mira 4. This is the message I receive. Any suggestions. Thanks. Marija Tauschek -- Dr Marija Tauschek/Atanaskovic Robins-Browne Lab Dept Microbiology & Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia Tel: +61 3 8344 9927 Email: matan(a)unimelb.edu.au Internal Server Error Galaxy was unable to successfully complete your request URL: http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https… Module galaxy.web.framework.middleware.error:149 in __call__ >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> app_iter = self.application(environ, sr_checker) Module paste.recursive:84 in __call__ >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> body = method( trans, **kwargs ) Module galaxy.web.framework:369 in decorator >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:983 in prepare_for_install >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> includes_tool_dependencies ) Module tool_shed.util.common_install_util:97 in get_dependencies_for_repository >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repository_owner, changeset_revision ) Module tool_shed.util.shed_util_common:1036 in get_repository_for_dependency_relationship >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> ( name, owner, changeset_revision ) ) Module tool_shed.util.shed_util_common:1867 in url_join >> <http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> parts.append( arg.strip( '/' ) ) AttributeError: 'NoneType' object has no attribute 'strip' extra data<http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> full traceback<http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> text version<http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https…> This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.

2 2

Database integrity error when installing new tools from toolshed
by Michael Ta 22 Aug '14

22 Aug '14

Hi, I updated a local Galaxy installation a while back and I followed the steps listed on one of the wiki pages. The update included changes to the database schema and I was careful to backup and restore it according to the directions. However, when I try to install new tools from the tool shed or update a tool to a new revision it does not complete successfully. The following error appears in the log file. File '/home/galaxy/galaxy-dist/lib/tool_shed/util/tool_util.py', line 761 in handle_tool_versions context.flush() File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py', line 114 in do File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 1718 in flush File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 1789 in _flush File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.p y', line 331 in execute File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.p y', line 475 in execute File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence. py', line 64 in save_obj File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence. py', line 558 in _emit_insert_statements File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', line 1449 in execute File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', line 1584 in _execute_clauseelement File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', line 1698 in _execute_context File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', line 1691 in _execute_context File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.p y', line 331 in do_execute IntegrityError: (IntegrityError) duplicate key value violates unique constraint "tool_version_association_pk ey" DETAIL: Key (id)=(83) already exists. 'INSERT INTO tool_version_association (tool_id, parent_id) VALUES (%(tool_id)s, %(parent_id)s) RETURNING to ol_version_association.id' {'parent_id': 440, 'tool_id': 439} A few of the keys appear to be colliding with values already in the database, did I miss something when I updated and restored the database that is causing this? Thanks, -- Michael Ta

2 2

Galaxy and HTTPS User-authentification
by Matthias Enders 22 Aug '14

22 Aug '14

Hi, I have a question regarding the user authentication of Galaxy. As to my knowledge galaxy uses http, also for the authentication, so the User Email and the password are send in clear text. As I like to use Galaxy for user-authentication and due several disadvantages not an external authentification like described here (https://wiki.galaxyproject.org/Admin/Config/ExternalUserDatbases): Is there any way of using https or an encryption-method for sending user email and password. With kind regards, Matthias Enders

2 1

Problems downloading files via bioblend
by Brad Zeitner 22 Aug '14

22 Aug '14

I have a python script that I use to download the qc data generated in one of the steps in a workflow. It used to work on a previous install of galaxy - but we've gone through and updated our Galaxy install so that it's now running on a new file system - and when I try and use the bioblend api to download the dataset the request for the file gets redirected to the login page. The call to download it is - dm = gi.datasets.download_dataset(qcf.get("id"), outfile, False ) Where qcf is the history step This calls the following url:/datasets/4fa2da3cf0e735a4/display?to_ext=html If I visit the url in a browser that's not in a session, it behaves the same way - but works correctly when I am logged in. How can I access this using the api key? When I add the parameters key=${myKey} it still fails. Thanks, -Brad Zeitner ________________________________ --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org

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Re: [galaxy-dev] Internal Server Error when trying to install a tool from the Tool shed
by John Chilton 22 Aug '14

22 Aug '14

Hello Audrey, Please keep responses on list - it ensures people smarter than me can respond :). Can you tell me what is sitting in front of Galaxy - Apache, Nginx, uwsgi, etc... and send the configurations if possible? I believe the out-of-the-box uwsgi configuration has some problems with really long URL query strings which using the tool shed does produce. -John On Mon, Aug 18, 2014 at 11:56 AM, audrey michel <audreymannion(a)gmail.com> wrote: > Hi John, > > We tried the following on another server where there is no proxy, and we are > able to install tools from this new instance: > > > hg clone https://bitbucket.org/galaxy/galaxy-dist/ > > > $ hg clone https://bitbucket.org/galaxy/galaxy-dist/ > destination directory: galaxy-dist > requesting all changes > adding changesets > adding manifests > adding file changes > added 14316 changesets with 48369 changes to 8546 files (+1 heads) > updating to branch default > 3597 files updated, 0 files merged, 0 files removed, 0 files unresolved > > We then modified just the admin_users, tool_dependency_dir, port and > localhost. This was sufficient to allow us to use the toolshed to install > tools on this particular instance of galaxy. > > So it would appear to be a proxy issue with our other instance of galaxy > which is behind a proxy. Could you advise us on where we need to add > http_proxy as we don't know which file(s) to add this to? We already set the > filter-with = proxy-prefix in the universe_wsgi.ini fiel. > > Thanks in advance, > Audrey > > > > > > > > > On Mon, Aug 18, 2014 at 11:31 AM, audrey michel <audreymannion(a)gmail.com> > wrote: >> >> Hi John, >> >> Thanks for the suggestions. We are going to try a new install on one of >> our other servers and see if the problem occurs there or not. >> >> Will update you when we do this. >> >> Thanks. >> Audrey >> >> >> On Fri, Aug 15, 2014 at 8:20 PM, John Chilton <jmchilton(a)gmail.com> wrote: >>> >>> Okay - I am replying in thread but I not to your original message >>> because there might be private stuff in the log you sent me. It looks >>> like you were trying to install fastqdump from the main tool shed. So >>> I setup a fresh Galaxy instance this morning and the only two things I >>> changed in the universe_wsgi.ini file were admin_users and >>> tool_dependency_dir (required to install tool dependencies) and this >>> install worked for me. Your error message had "Bad Status Line" in it >>> - so it sounds like you were getting non-sense back from the tool >>> shed. >>> >>> This could be because there is some proxy interfering with this >>> request, it could be that it was just an intermittent problem with the >>> tool shed, or ... some configuration problem potentially? I am not >>> sure. >>> >>> It looks like you had cloned galaxy-dist directly - I think it is >>> better to stay on a particular branch - I would do this: >>> >>> hg pull >>> hg update latest_2014.08.11 >>> >>> To make sure you have the latest and greatest Galaxy and then retry? >>> >>> If you still have problems and it is the same strack trace - please >>> let me know. Next up would be to eliminate the proxy theory - not sure >>> how to do that though :(. >>> >>> -John >>> >>> On Wed, Aug 13, 2014 at 4:36 PM, John Chilton <jmchilton(a)gmail.com> >>> wrote: >>> > I am not sure what the problem is - more details would really help. >>> > For instance - What version of Galaxy are you using? What repository >>> > are you trying to install? Do other repositories work? Does the Galaxy >>> > log have a more complete stack trace? >>> > >>> > Any additional details would be most helpful. >>> > >>> > Thanks, >>> > -John >>> > >>> > On Tue, Aug 12, 2014 at 9:11 AM, audrey michel >>> > <audreymannion(a)gmail.com> wrote: >>> >> Hi, >>> >> >>> >> We get the following error when we try to install any tool from the >>> >> Tool >>> >> shed when using the Admin panel: >>> >> >>> >> >>> >> Internal Server Error >>> >> >>> >> Galaxy was unable to successfully complete your request >>> >> >>> >> An error occurred. >>> >> >>> >> This may be an intermittent problem due to load or other unpredictable >>> >> factors, reloading the page may address the problem. >>> >> >>> >> The error has been logged to our team. >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> We would be grateful if you could advise on this issue. >>> >> >>> >> Kind Regards, >>> >> Audrey Michel >>> >> Baranov Lab >>> >> School of Biochemistry & Cell Biology >>> >> University College Cork >>> >> Ireland >>> >> >>> >> >>> >> >>> >> ___________________________________________________________ >>> >> 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: >>> >> http://lists.bx.psu.edu/ >>> >> >>> >> To search Galaxy mailing lists use the unified search at: >>> >> http://galaxyproject.org/search/mailinglists/ >> >> >

2 3

bioblend run_workflow (no_wait?)
by Evan Bollig 21 Aug '14

21 Aug '14

I'm using bioblend to launch a workflow, but i find that the gi.workflows.run_workflow() command does not provide an option for no_wait. Can anyone provide justification for why this needs to be synchronous? -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

2 3

Problem uploading files to RNA-Rocket
by David Salcines 21 Aug '14

21 Aug '14

Hi, I was trying to upload some FASTQ files via FTP using the FileZilla client but although the program connects to the server it doesn't log in. I checked the user and the password several times and I tried to use another account but I still got the same error. I also tried to upload the files via URL (using Mega) but when the upload is finished the files appear to be empty. Thanks David

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galaxy-dev August 2014