- galaxy-dev - lists.galaxyproject.org

psiblast
by Luobin Yang 11 Feb '13

11 Feb '13

Hi, Galaxy developers, I do not see a web interface for psi-blast in NCBI BLAST+ in the tool shed. Does it have one? Thanks, Luobin

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Galaxy February 8, 2013 Distribution & News Brief
by Jennifer Jackson 08 Feb '13

08 Feb '13

Galaxy Feb 8, 2013 Distribution & News Brief <http://wiki.galaxyproject.org/News/2013_02_08_GalaxyNewsBrief> *Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2013_02_08> * *Highlights:* * /Improvements/ to our release process <http://wiki.galaxyproject.org/DevNewsBriefs/2013_02_08#Improvements_to_Rele…>. *Release tag must be used in the hg update command to upgrade*. More at *usegalaxy.org <http://wiki.galaxyproject.org/Admin/Get%20Galaxy>*. * Tool Shed /Complex repository dependencies/ <http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Complex_reposi…> are introduced, streamlining core dependency use across individual tools. * Also updated in the Tool Shed: multiple repository installation, dependency installation (when defined), and many usability enhancements and fixes. * New /Bedgraph-to-bigwig/ <http://wiki.galaxyproject.org/Learn/Datatypes#BedGraph> tool plus /Filter/ tool updated. * /Workflows/ now include option to export an image and the core /Framework/ now allows more unified reference genome usage and access. * /Ten Community Pull-Requests/ incorporated, plus another contribution to the tool Shed, addressing general usability, API, tools, error handling, workflows, and more. Thanks!! * Review highlights from the latest monthly */Galaxy Update/* <http://wiki.galaxyproject.org/GalaxyUpdates> newsletter and Galaxy Project Stats <http://wiki.galaxyproject.org/Galaxy%20Project/Statistics>! * Plus bug fixes and related enhancements for visualizations, histories, workflows, and tools. *http://getgalaxy.org* *http://bitbucket.org/galaxy/galaxy-dist* *http://galaxy-dist.readthedocs.org * new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull $ hg update release_2013.02.08 To ensure that you continue to receive updates about *Galaxy Distributions and News Briefs* <http://wiki.galaxyproject.org/DevNewsBriefs>, be sure to subscribe to the Galaxy-Announce mailing list <http://wiki.galaxyproject.org/MailingLists#The_lists>, a low-volume list dedicated to News Items <http://wiki.galaxyproject.org/News> and priority messages from the Galaxy community <http://wiki.galaxyproject.org/Community> and project core team <http://wiki.galaxyproject.org/Galaxy%20Project>. /Thanks for using Galaxy,/ The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team>

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Error in database after trying the innocently named, but devastatingly evil "test" in manage_db.sh
by Thon de Boer 08 Feb '13

08 Feb '13

Hi, I had a small issue with the total usage of my galaxy system showing some negative random number so I figured my database was a little “off”. I snooped around for some database management tools and found “manage_db.sh” which had an option innocently called “test”. I ran it, without reading the little fine print that states: “Performs the upgrade and downgrade option on the given database. This is not a real test and may leave the database in a bad state. You should therefore better run the test on a copy of your database.” Well…It surely did leave my database in a bad state since now I get this when I try to access the toolshed installed tools: Error Traceback: View as: <http://srv151/admin_toolshed/browse_repositories> Interactive | <http://srv151/admin_toolshed/browse_repositories> Text | <http://srv151/admin_toolshed/browse_repositories> XML <http://srv151/admin_toolshed/browse_repositories> (full) ⇝ ProgrammingError: (ProgrammingError) relation "repository_repository_dependency_association" does not exist LINE 2: FROM repository_repository_dependency_association ^ 'SELECT repository_repository_dependency_association.id AS repository_repository_dependency_association_id, repository_repository_dependency_association.create_time AS repository_repository_dependency_association_create_time, repository_repository_dependency_association.update_time AS repository_repository_dependency_association_update_time, repository_repository_dependency_association.tool_shed_repository_id AS repository_repository_dependency_association_tool_shed_re_1, repository_repository_dependency_association.repository_dependency_id AS repository_repository_dependency_association_repository_d_2 \nFROM repository_repository_dependency_association \nWHERE %(param_1)s = repository_repository_dependency_association.tool_shed_repository_id' {'param_1': 5} URL: <http://srv151/admin_toolshed/browse_repositories> http://srv151/admin_toolshed/browse_repositories Is there ANY way I can rescue this fiasco? Suffice it to say I did not do it on a copy and did not do a backup (yes, I learned my lesson), but maybe some SQL skullduggery can help me? Thanks Thon

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Extract genomic DNA job error
by Perez, Ricardo 08 Feb '13

08 Feb '13

Hello, I am getting this error when using Extract Genomic DNA (version 2.2.2) empty format: fasta, database: hg19 924 warnings, 1st is: Chromosome by name 'chr22' was not found for build 'hg19'. Skipped 924 invalid lines, 1st is #1, "chr22 16256331 16287937 NM_001136213 0 - 16258185 16287885 0 11 346,119,167,45,71,71,138,107,174,115,684, 0,1853,10597,11805,13541,188 We set up a local instance of Galaxy and a local mirror of the UCSC Table browser in our servers. Thank you for your help, --Ricardo Perez

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Dependencies on other Tool Shed repositories
by Peter Cock 08 Feb '13

08 Feb '13

Hi all, I've been reading http://wiki.galaxyproject.org/ToolShedToolFeatures and focused on the example of EMBOSS where the tool definitions depend on the data type definitions. Here the emboss_5 repository (the tool wrappers) contains depository_dependencies.xml saying: <?xml version="1.0"?> <repositories description="Emboss 5 requires the Galaxy applicable data formats used by Emboss tools."> <repository toolshed="http://toolshed.g2.bx.psu.edu" name="emboss_datatypes" owner="devteam" changeset_revision="a89163f31369" /> </repositories> Is that revision treated as a minimum version, or an absolute one? This concerns me as I have three repositories which will all depend on the blast_datatypes repository for the 'blastxml' format (etc) - so what happens when these three repositories don't all request the same revision of the blast_datatypes repository? What I'm using for now is: <?xml version="1.0"?> <repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format).">  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="blast_datatypes" owner="devteam" changeset_revision="f9a7783ed7b6" /> </repositories> Regards, Peter

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Desire to contribute
by Matthew Paul 08 Feb '13

08 Feb '13

Dear Galaxy Project community,

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Error when trying to change the permissions in data libraries.
by Christos Kannas 08 Feb '13

08 Feb '13

Hi, In our local Galaxy server an error came up today. When I try to edit the permissions of data librarles via the Admin panel I get the following error: (Also attached is an image of the following error) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 0: ordinal not in range(128) URL: http://lisis.cs.ucy.ac.cy/library_common/library_permissions?show_deleted=F… File '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/library_common.py', line 262 in library_permissions status=status ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 832 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 843 in fill_template_mako return template.render( **data ) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/home/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/home/galaxy/galaxy-dist/database/compiled_templates/library/common/ library_permissions.mako.py', line 76 in render_body __M_writer(unicode(render_permission_form( library, library.name, h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted ), roles, do_not_render=[], all_roles=all_roles ))) File '/home/galaxy/galaxy-dist/database/compiled_templates/dataset/ security_common.mako.py', line 108 in render_render_permission_form __M_writer(unicode(render_select( current_actions, k, v, all_roles ))) File '/home/galaxy/galaxy-dist/database/compiled_templates/dataset/ security_common.mako.py', line 34 in render_select return render_render_select(context,current_actions,action_key,action,roles) File '/home/galaxy/galaxy-dist/database/compiled_templates/dataset/ security_common.mako.py', line 190 in render_render_select __M_writer(unicode(role.name)) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 0: ordinal not in range(128) We are using a modified version of Galaxy. The info from hg (latest galaxy-dist we have pulled): changeset: 7828:b5bda7a5c345 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Oct 05 15:49:26 2012 -0400 summary: Fix the Compute tool to only allow for execution of a limited set of expressions. What we have to do to fix it? Thanks, Christos -- Christos Kannas Researcher Ph.D Student e-Health Laboratory <http://www.medinfo.cs.ucy.ac.cy/> kannas.christos(a)ucy.ac.cy kannas.christos(a)cs.ucy.ac.cy chriskannas(a)gmail.com

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Fwd: Multiple Instances ...
by Ross 07 Feb '13

07 Feb '13

ok - sorry I misunderstood. Yes, assuming you already have one Galaxy instance configured right, cloning and editing the rewrite and authentication sections for the other paste process should work and that looks reasonable to me FWIW - OTOH, apache configuration is definitely one of the darker arts so the only way to tell is to run them and keep an eye on the two separate paste process logs as you hit each site separately. Of course, make sure the indepndent instance universe_wsgi.xml files specify independent postgresql databases and keep the two independent galaxy file store directories separated or very bad things will happen. On Fri, Feb 8, 2013 at 2:20 PM, <Neil.Burdett(a)csiro.au> wrote: > Thanks Ross.**** > > ** ** > > I did mean separate Galaxy instances like test and main with their own > independent backend databases.**** > > ** ** > > How could I run say a test and a main from the same node? **** > > ** ** > > I guess I’d need to modify the port number for each instance and then > multiple entries in the apache config file i.e. So they show physically > separate information when loaded... i.e. http://localhost/galaxyTest and > . http://localhost/galaxyMain**** > > ** ** > > *RewriteEngine* *on***** > > *RewriteRule* ^/galaxyTest$ */galaxyTest/* [R]**** > > *RewriteRule* ^/galaxyTest/static/style/(.*) * > /home/nate/galaxy-dist-test/static/june_2007_style/blue/*$1 [L]**** > > *RewriteRule* ^/galaxyTest/static/scripts/(.*) * > /home/nate/galaxy-dist-test/static/scripts/packed/*$1 [L]**** > > *RewriteRule* ^/galaxyTest/static/(.*) * > /home/nate/galaxy-dist-test/static/*$1 [L]**** > > *RewriteRule* ^/galaxyTest/favicon.ico * > /home/nate/galaxy-dist-test/static/favicon.ico* [L]**** > > *RewriteRule* ^/galaxyTest/robots.txt * > /home/nate/galaxy-dist-test/static/robots.txt* [L]**** > > *RewriteRule* ^/galaxyTest (.*) http://localhost:9080$1 [P]**** > > ** ** > > *RewriteRule* ^/galaxyMain$ */galaxyMain/* [R]**** > > *RewriteRule* ^/galaxyMain/static/style/(.*) */home/nate/galaxy-dist-main/static/june_2007_style/blue/*$1 [L]**** > > *RewriteRule* ^/galaxyMain/static/scripts/(.*) */home/nate/galaxy-dist-main/static/scripts/packed/*$1 [L]**** > > *RewriteRule* ^/galaxyMain/static/(.*) */home/nate/galaxy-dist-main/static/*$1 [L]**** > > *RewriteRule* ^/galaxyMain/favicon.ico */home/nate/galaxy-dist-main/static/favicon.ico* [L]**** > > *RewriteRule* ^/galaxyMain/robots.txt */home/nate/galaxy-dist-main/static/robots.txt* [L]**** > > *RewriteRule* ^/galaxyMain (.*) http://localhost:9081$1 [P]**** > > ** ** > > Is that correct?**** > > ** ** > > Cheers**** > > Neil**** > > ** ** > > ** ** > > *From:* Ross [mailto:ross.lazarus@gmail.com] > *Sent:* Friday, 8 February 2013 12:54 PM > *To:* Burdett, Neil (ICT Centre, Herston - RBWH) > *Cc:* galaxy-dev(a)lists.bx.psu.edu > *Subject:* Re: [galaxy-dev] Multiple Instances ...**** > > ** ** > > Neil, **** > > ** ** > > If by 'multiple' you mean 'independent' galaxy instances, they must each > talk to independent backend databases, so if you're thinking of running eg > 2 or more independent instances at CSIRO, each for specific tool sets and > sending each of your users to one or other of them based on some smart > Apache code and their login, beware that users won't be able to share or > see any histories or datasets from one instance on the other. **** > > ** ** > > That might work well - or not - but separate instances cannot safely share > the same backend database tables - they're just separate Galaxy instances - > like test and main are, and there's no specific documentation needed.**** > > ** ** > > If you are asking about multiple processes (web servers etc) to scale up a > slow heavily loaded instance, that's documented in the wiki - eg a quick > search finds > http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?act… > **** > > ** ** > > On Fri, Feb 8, 2013 at 1:40 PM, <Neil.Burdett(a)csiro.au> wrote:**** > > Hi,**** > > Can someone point me to the documentation to set up /configure multiple > instances of Galaxy running on the same node please?**** > > **** > > I think this is the best method of hiding tools based upon users email > logon...**** > > **** > > Thanks**** > > Neil**** > > ** > -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ

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Multiple Instances ...
by Neil.Burdett＠csiro.au 07 Feb '13

07 Feb '13

Hi, Can someone point me to the documentation to set up /configure multiple instances of Galaxy running on the same node please? I think this is the best method of hiding tools based upon users email logon... Thanks Neil

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What image formats can be displayed in the Galaxy view panel?
by Luobin Yang 07 Feb '13

07 Feb '13

Hi, I tried the pcx and ps formats, but the browser just downloads these kinds of files instead rendering them in the Galaxy window... It seems png and pdf files can be rendered in the Galaxy windows. How can I make Galaxy display other image formats like ps and pcx? Thanks, Luobin

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