galaxy-dev October 2013

galaxy-dev@lists.galaxyproject.org

112 participants
166 discussions

worflow editor is slow with a large amount of steps
by Bjoern Gruening 21 Oct '13

21 Oct '13

Hi, one of our users has created a large workflow with > 300 steps. Yes he really loves Galaxy :) Unfortunately, its not possible to use the graphical user interface anymore with so many steps. You can't connect boxes and scrolling is also slow. It there any hint how to solve, any workflow redesign already planned or in preparation? I would spend some time in improving it if it's worth. Any pointer to the used Javascript library, or is that mainly solved with the "workflow in a workflow" GSOC project that was merged recently. Trello card is here: https://trello.com/c/dgVrxrHC Cheers, Bjoern

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Re: [galaxy-dev] page editor problem when saving Chinese
by lardo 21 Oct '13

21 Oct '13

My local instance's version was the latest version(I downloaded last night), but this problem can't be fixed. lardo@ubuntu:~/galaxy-dist$ hg pull -u pulling from https://bitbucket.org/galaxy/galaxy-dist/ searching for changes no changes found ------------------ Original ------------------ From: "Jeremy Goecks";<jeremy.goecks(a)emory.edu>; Date: Sat, Oct 19, 2013 05:28 AM To: "lardo"<lardo(a)qq.com>; Cc: "galaxy-dev"<galaxy-dev(a)lists.bx.psu.edu>; Subject: Re: [galaxy-dev] page editor problem when saving Chinese This issue was fixed in this changeset: https://bitbucket.org/galaxy/galaxy-central/commits/8c663e656f64a60dac55979… If you update your Galaxy to the revision on galaxy-dist this problem should go away. Best, J. On Oct 18, 2013, at 1:10 PM, lardo <lardo(a)qq.com> wrote: I run a local instance of galaxy and edit content of a page, error occurs when the content contains Chinese: URL: http://127.0.0.1:8080/page/save Module weberror.evalexception.middleware:364 in respond >> app_iter = self.application(environ, detect_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.web.framework:98 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.page:566 in save >> trans.sa_session.flush() Module sqlalchemy.orm.scoping:114 in do Module sqlalchemy.orm.session:1718 in flush Module sqlalchemy.orm.session:1789 in _flush Module sqlalchemy.orm.unitofwork:331 in execute Module sqlalchemy.orm.unitofwork:475 in execute Module sqlalchemy.orm.persistence:64 in save_obj Module sqlalchemy.orm.persistence:558 in _emit_insert_statements Module sqlalchemy.engine.base:1449 in execute Module sqlalchemy.engine.base:1584 in _execute_clauseelement Module sqlalchemy.engine.base:1698 in _execute_context Module sqlalchemy.engine.base:1691 in _execute_context Module sqlalchemy.engine.default:331 in do_execute ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings. u'INSERT INTO page_revision (create_time, update_time, page_id, title, content) VALUES (?, ?, ?, ?, ?)' ('2013-10-18 17:09:01.226991', '2013-10-18 17:09:01.227000', 1, u'test', 'aavdx\xe4\xb8\xad') [] ___________________________________________________________ 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/

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Input parameter validation dependent on another parameter?
by Peter Cock 21 Oct '13

21 Oct '13

Hello all, I'm currently trying to define a pair of integer parameters for min/max values: <param name="min_size" type="integer" optional="true" min="0" value="" label="Minimum" help="Optional, but if used you must also supply a maximum value." /> <param name="max_size" type="integer" optional="true" min="0" value="" label="Maximum" help="Optional, but if used you must also supply a minimum value." /> As far as I can tell from the documentation, there is no way to write a validator which links the two parameters, for example in order to insist that min_size <= max_size? http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Alternatively, is it possible in the Cheetah section to raise an exception? That way at least the error should happen almost immediately (without having to wait for the cluster queue etc), e.g. raise ValueError("Requires minimum size is less than maximum!") Or, perhaps this particular use-case is common enough to warrant a new param type="integer-range" which shows two text boxes? Thanks, Peter

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Error on Get Data
by Jurgens de Bruin 21 Oct '13

21 Oct '13

I get the follow error on my local installation.... 9: UCSC Main on Pig: refGene (chr18:1-61220071) error An error occurred with this dataset: *Traceback (most recent call last): File "/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/tools/data_source/data_source.py", line 8, in import galaxy.model # need to import model before sniff to resolve a circular import dependency* Any help would be appreciated.... -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin

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impersonation - history - error?
by Nikolai Vazov 21 Oct '13

21 Oct '13

Hi I am running release_2013.06.03 I used the feature "impersonate user", logged out without a problem but the user's history is still displayed along with my own history. How do I get rid of it. Deletion of jobs/files also deletes them from the users history :) Thank you in advance Nikolay -- Nikolay Vazov, PhD Research Computing Centre - http://hpc.uio.no USIT, University of Oslo

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Functional tests results in Invalid HTTP return code 404/500, allowed codes: 200
by Serrano Pereira 19 Oct '13

19 Oct '13

Dear Galaxy hackers, I'm having trouble with the tool test framework. I have a local installation of a Galaxy Tool Shed (latest stable from the repository) on my Linux server. I have an Apache proxy to my tool shed (per http://wiki.galaxyproject.org/HostingALocalToolShed). The Tool Shed seems to work fine. I'm able to create and maintain repositories and I'm able to install tools from the Tool Shed from remote Galaxy instances. Now I want to run the functional tests of the tools in the Tool Shed. I do that by following the instructions on the wiki (http://wiki.galaxyproject.org/AutomatedToolTests). It comes down to the following commands: ---------------------------------------------------------------------- cd /opt/galaxy/galaxy-dist/ export GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY=2aeecfe2d9f28d0c5b6959a41886b5fd export GALAXY_INSTALL_TEST_TOOL_SHED_URL=http://toolshed.galaxy.domain.org/ python lib/tool_shed/scripts/check_repositories_for_functional_tests.py tool_shed_wsgi.ini sh install_and_test_tool_shed_repositories.sh ---------------------------------------------------------------------- The second script (install_and_test_tool_shed_repositories.sh) fails with the following error: ====================================================================== FAIL: install_repository_usearch (install_and_test_tool_shed_repositories.functional.test_install_repositories.TestInstallRepository_usearch) Install the repository usearch from http://toolshed.galaxy.domain.org/. ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/galaxy/galaxy-dist/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py", line 48, in test_install_repository self.do_installation( repository_dict ) File "/opt/galaxy/galaxy-dist/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py", line 17, in do_installation self.install_repository( repository_info_dict ) File "/opt/galaxy/galaxy-dist/test/install_and_test_tool_shed_repositories/base/twilltestcase.py", line 61, in install_repository self.visit_url( '%s/repository/preview_tools_in_changeset?%s' % ( tool_shed_url, preview_params ) ) File "/opt/galaxy/galaxy-dist/test/install_and_test_tool_shed_repositories/base/twilltestcase.py", line 112, in visit_url ( return_code, url, ', '.join( str( code ) for code in allowed_codes ) ) AssertionError: Invalid HTTP return code 404 for http://toolshed.galaxy.domain.org//repository/preview_tools_in_changeset?re…, allowed codes: 200 ---------------------------------------------------------------------- (I've changed twilltestcase.py to also print the URL that is being browsed.) This is were it get's weird. The HTTP 404 response code indicates that the page was not found. However, when I browse to that URL, it works fine! What's more, when I try to access that page with `wget` from the same machine the HTTP response code is 200: ---------------------------------------------------------------------- wget http://toolshed.galaxy.domain.org//repository/preview_tools_in_changeset?re… ... HTTP request sent, awaiting response... 200 OK ... ---------------------------------------------------------------------- When I use the Tool Shed URL http://localhost:9009/ instead, I get a similar error, only the return code is 500 instead of 404. I suspect that the HTTP return code returned by the Python module that returns it (Mechanize?) is invalid. I found a note about this error on the wiki (http://wiki.galaxyproject.org/Admin/Running%20Tests): "Note: If you have another version of paste installed in your PYTHONPATH, it can cause problems running the functional tests. Many tests will error (instead of passing/failing) because of an HTML code 500 where a 200 was expected. There are two workarounds for this: uninstall paste or use virtualenv. " The thing is, I do not have another version of Paste installed. What can I do to fix this error? Regards, Serrano Pereira

2 5

page editor problem when saving Chinese
by lardo 18 Oct '13

18 Oct '13

I run a local instance of galaxy and edit content of a page, error occurs when the content contains Chinese: URL: http://127.0.0.1:8080/page/save Module weberror.evalexception.middleware:364 in respond >> app_iter = self.application(environ, detect_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.web.framework:98 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.page:566 in save >> trans.sa_session.flush() Module sqlalchemy.orm.scoping:114 in do Module sqlalchemy.orm.session:1718 in flush Module sqlalchemy.orm.session:1789 in _flush Module sqlalchemy.orm.unitofwork:331 in execute Module sqlalchemy.orm.unitofwork:475 in execute Module sqlalchemy.orm.persistence:64 in save_obj Module sqlalchemy.orm.persistence:558 in _emit_insert_statements Module sqlalchemy.engine.base:1449 in execute Module sqlalchemy.engine.base:1584 in _execute_clauseelement Module sqlalchemy.engine.base:1698 in _execute_context Module sqlalchemy.engine.base:1691 in _execute_context Module sqlalchemy.engine.default:331 in do_execute ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings. u'INSERT INTO page_revision (create_time, update_time, page_id, title, content) VALUES (?, ?, ?, ?, ?)' ('2013-10-18 17:09:01.226991', '2013-10-18 17:09:01.227000', 1, u'test', 'aavdx\xe4\xb8\xad') []

2 1

Zero padding corruption using galaxy with torque on AFS
by Renato Alves 18 Oct '13

18 Oct '13

Hi everyone, I'm currently setting up galaxy to run on top of AFS using torque for handling jobs. Everything is setup according to wiki documentation but I'm having a weird filesystem corruption problem. The setup is the following: machine A: runs galaxy. Galaxy home folder is on AFS. machine B: runs torque server and shares Galaxy's home folder. When I launch a process via galaxy everything works as expected but the output file becomes corrupted with 4kb of leading zero bytes (file NC_010473.tabular). This corruption is reproducible at all times, regardless of file size. In the attached example, the original file is NC_010473.faa. If I restart the openafs client or flush the AFS file cache the corruption goes away. However, if I re-run the same script created by galaxy through torque the corruption doesn't happen. Hence it only happens if launched via Galaxy. I also tried both the DRMAA and the PBS modules but the corruption remained. Does anyone know what could be the cause of this? Thanks, Renato

1 1

file download returns empty file or webpage error
by UMD Bioinformatics 17 Oct '13

17 Oct '13

Hello, I've looked through the archives and I see that this issue has been raised before (http://dev.list.galaxyproject.org/file-download-returns-empty-file-or-webpa…) but without a noted resolution. I am running Apache as proxy but I downloads from multiple machines and browsers are either empty or return an error after clicking the download button. I enabled Apache xsend file: <Location "/"> XSendFile on XSendFileAllowAbove on XSendFilePath /galaxy </Location> And configured galaxy to be aware of this in universe_wsgi.ini apache_xsendfile = True. I have checked the apache error logs and do not see any issues reported. Any help would be appreciated. I've ended up changing apache_xsendfile = false just so that i can download data. How do I get galaxy apache and xsendfile to work properly? Cheers, Ian

1 0

RFC: remove trailing semicolons from command line -> Broken bowtie2_wrapper on some SGE systems
by Björn Grüning 17 Oct '13

17 Oct '13

Dear all, some SGE instances will add automatically an semicolon add the end of each command, resulting in a disrupted job, because ';;' are not allowed. The latest changes to the Bowtie2 wrapper resulting in such a case and a crash in our instance. An easy solution would be to fix the wrapper and omitting the trailing ';' but maybe its better to fix it once for all in the corresponding tools code, patched attached. I'm not familiar with other Job schedulers so I'm seeking for comments ... it there any disadvantage of removing trailing ';' from the command line? Ciao, Bjoern

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galaxy-dev October 2013