- galaxy-dev - lists.galaxyproject.org

display at third party tools error
by TerryYeh＠NARL 22 Oct '13

22 Oct '13

I have a question about sending a bed to Ensembl or bam to IGV through Galaxy. I have setup a galaxy on my own pccluster. Everything is fine. But when I want to display the bam file to IGV, I got the error message about error loading files. "Error loading http://xxx.xx.xxx/galaxy/display_application/xxxxxxxxxx/data/galaxy_xxxxx.ba m: An error occurred while accessing: http://xxx.xx.xxx/galaxy/display_application/xxxxxxxxxx/data/galaxy_xxxxx.ba m Read error; BinaryCode in readmode; streamed file (filename not available)" When I use the url to get the file directly, it can be successfully downloaded. I meet the same situation when I send the bed file to display at Ensembl. The tract will not be shown on Ensembl. When I want to send the bed manually through url, I also get the error message about loading files. "Unable to access file. Server response: 500 read timeout" Does anyone know how to solve the problem?? Thanks a lot!! Best Regards, Terry Yeh

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Share workflows for all users
by Anatoliy Pandorin 22 Oct '13

22 Oct '13

For a long time I used release_2013.01.13. And to share workflows for all users galaxy used a simple link to workflow (exp: <url>/workflow/run?id=cbbbf59e8f08c98c ) This was done by my simple script. (copied links to "welcome" page) Moving on release_2013.08.12 this method does not work anymore. You first need add users to "Share Workflow with Individual Users". It is without a doubt correct. But: As now distribute(Share) workflow for all users at once? Maybe I do not understand that. Pardon Best regards, Anatoly

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Workflow step dependencies
by Eric Rasche 21 Oct '13

21 Oct '13

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello all, At my organisation's instance of galaxy, we have some connectors to talk to chado (inserting/removing GenBank & GFF files, etc). However, for one of the workflows we plan to use, there is a script which must be run which has no input files and no output files (gmod_add_organism.pl, for those curious). This script *must* be run before another script is run (gmod_bulk_load_gff3.pl), or the database insert will fail So my question is: Is there an easy way to specify dependencies when they depend on external factors, rather than just input/output files? If there isn't a generalised mechanism to do this, should I just list input and output files that are never actually created or removed? Cheers, Eric - -- Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr(a)tamu.edu rasche.eric(a)yandex.ru -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJSZWA0AAoJEMqDXdrsMcpVGBUP/izaBVdCMR8ezm+5GNDpbsiZ CohkkFFZluewd14a08Mmgv42atmqAD10YiJAr1p5xu2eDB5OQJSH7dqXEbAS3IaL IhmfCkZdyd/+FUbOHwcS1AQ/XGWCQlahoME3sPsNOJM0Ru1jwA/Z4w7+CwZ0VSmy ooqExkS87S3wLzzflivqBnu40de1vWt33mIIbPRUDukPHQRPZMDNRPtAhUE2mL52 nkuUfhgcSNjyIYnCEqCNq5xd+sACepLB5F3LtszdmMgd9jjAJVcXqeXugiN4TSeI arMlzmPq2uIhDNKqx/ljsA9GqgrsLI+WJ2EvbTirAAvbcPVZDUCEMuRc7tMluSfp J8wU4wu2h2J3KvTIbOYiP0eudTTzDdfBvkNV4Zdvygv9WdNutFbLvwiNMt7FiUVI gq3/Mq95J74UahL9NeuG02vpMCRChigMG6cXjCaZfAlnubjbdLZ56XF/XVQeRaoz MnW35R7Y3ER46eFzSq6hU1Xlsjq2I5Esm4yx2O5Rs7Ieu4MSHdz7SV6qkGX32dVC ajSfue/zPd4DEj83mFrZjcjpax7YNF006CrWyBftC5dPKWfftuqy1Uhl2EZuscPI I8dliTrT0DIHJX5GqhqoMuX4iq5rN1WhSVB0N+HQZDt1nhHyiWyO/7zb0n6sHPv/ E9D2qOO7jYL++b6oTIT9 =RQ0Y -----END PGP SIGNATURE-----

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Main tool shed is running the next-stable branch
by Greg Von Kuster 21 Oct '13

21 Oct '13

FYI: The Main Tool Shed is now running the next-stable branch and all metadata has been reset on all repositories. The tentative date of the next Galaxy relesase is currently November 4. The Main Tool Shed will be updated to the stable branch at the time of the release. Greg Von Kuster

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Installation on cluster
by Jurgens de Bruin 21 Oct '13

21 Oct '13

Hi, I am struggling to get galaxy to submit job to a cluster, I am using Torque and Maui. This is my universe_wsgi.ini ----- Handler Definitions ------------------------------------------------- [server:web0] use = egg:Paste#http port = 8181 host = 127.0.0.1 use_threadpool = true threadpool_workers = 7 [server:web1] use = egg:Paste#http port = 8182 host = 127.0.0.1 use_threadpool = true threadpool_workers = 7 [server:handler0] use = egg:Paste#http port = 8090 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler1] use = egg:Paste#http port = 8091 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 # ------ Handler Definitions ------------------------------------------------- This is job_conf.xml *<?xml version="1.0"?>  <job_conf> <plugins workers="4"> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="6"/> </plugins> <handlers default="handlers"> <handler id="handler0" tags="handlers"/> <handler id="handler1" tags="handlers"/> </handlers> <destinations default="regularjobs"> <destination id="local" runner="local"/> <destination id="regularjobs" runner="pbs" tags="cluster"> <param id="Resource_List">walltime=24:00:00</param> <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> <destination id="real_user_cluster" runner="pbs"> <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> <destination id="dynamic" runner="dynamic">  <param id="type">python</param> <param id="function">interactiveOrCluster</param> </destination> </destinations> </job_conf><?xml version="1.0"?>  <job_conf> <plugins workers="4"> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="6"/> </plugins> <handlers default="handlers"> <handler id="handler0" tags="handlers"/> <handler id="handler1" tags="handlers"/> </handlers> <destinations default="regularjobs"> <destination id="local" runner="local"/> <destination id="regularjobs" runner="pbs" tags="cluster"> <param id="Resource_List">walltime=24:00:00</param> <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> <destination id="real_user_cluster" runner="pbs"> <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> <destination id="dynamic" runner="dynamic">  <param id="type">python</param> <param id="function">interactiveOrCluster</param> </destination> </destinations> </job_conf>* I can submit jobs to the cluster so I know that part is working. 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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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', '<p>aavdx</p><p>\xe4\xb8\xad</p>') [] ___________________________________________________________ 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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