March 2013 - galaxy-dev - lists.galaxyproject.org

Multicore
by Alexander Kurze 26 Mar '13

26 Mar '13

Hi there, we have a 32 core server but I realised that a lot of programs are only using a fraction of that. I was able to adjust bowtie, bowtie2 and Tophat to use all of the cores but couldn't find an thread/core option for Macs14, Macs2 or PeakRanger. Does anyone know if these programs are capable of multi threading? If yes, where do I adjust it? Would be nice to have some global parameter set in the universewgsi.ini file. Thanks, Alex

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hello Newbie questions about galaxy and clustering
by Jennifer Jackson 26 Mar '13

26 Mar '13

Hello Jereme, I am going to post your question over to the galaxy-dev(a)bx.psu.edu mailing list to give it better visibility to the development community. This is also where you will want to post future questions about your local install. http://wiki.galaxyproject.org/MailingLists For you question about cluster set-up: Starting at our basic install help: -> http://wiki.galaxyproject.org/Admin/Get%20Galaxy At the bottom of the page is a link "Running Galaxy in a production environment" that has help for getting your server set up to use a cluster: -> http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer The documentation for " Using a compute cluster" will then point to: -> http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster Now, we there is a release pending. I might be worth waiting a week or so for this, unless you are already pulling from galaxy-central (and not the galaxy-dist) repository, to avoid having to configure changes twice. If you have follow-up, please leave the question on the mailing list - the developers will have the best advice about details. Best, Jen Galaxy team On 3/26/13 6:25 AM, leconte wrote: > hello > I have installed an galaxy instance for purpose testing on a 8 CPU > server without problem all run perfectly. > I have made some galaxy xml wrapper to understant how galaxy calls > program and other little things. > > > Now I want to install a Galaxy server with a cluster configuration. > > > Before I have tested HTCondor but I have no Idea how I can mix > Galaxy and HTCondor. > > The perfect thing was somebody have already tested this type of condor. > > But I can satisfy myself with any other cluster type. > > What I don't understant in fact ( maybe my worst problem ) where lie > all parts of this puzzle. > > I explain. > > I know that I need Galaxy. I know too I need a cluster ( in my case > HTCondor ) > I understand I need something between these 2 parts ... I think > something like PBS or SGE but it's not totaly clear for me > > I'm search on galaxy mailling list archive ... but I just found 2 > mails in 2008 :( > > has anybody made this conf or have a configuration ? > > greetings > > PS : sorry for my poor english :) > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > 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/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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redirection vulnerability via URL injection
by Vipin TS 26 Mar '13

26 Mar '13

Hello dev-members, We are trying to place our public Galaxy instance<http://galaxy.raetschlab.org>in a more secured manner, Currently I am playing with few test cases about the redirection vulnerabilities. The following link uses a URL variable called “redirect_url” to redirect a user to a given page. While this variable is intended to only direct a user to a trusted page, it fails to validate the provided value and therefore can be used to redirect to any page. http://localhost:8080/datasets/332056/display_at/ucsc_test?redirect_url=htt… This example redirects a user to Google, but it could just as easily be used to direct a user to a page that contains any malware. To resolve the issue, may be validate all user controlled input, including the GET request variables. If the input is intended to redirect a user, it must be validated to ensure it only presents them with a page on the trusted site. any comments or suggestions to work around this. thanks --/Vipin Rätschlab, Computational biology dept. Memorial Sloan-Kettering Cancer Center

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Manage Local data
by Shaun Webb 26 Mar '13

26 Mar '13

Hi I am trying to load the mm10 genome and indexes using the manage local data admin feature. The genome downloads ok and so do the liftOver chain files, however the main controller and indexing jobs fail. They just display error, is there any way I can find out more about what is happening here and what is failing? Thanks Shaun Webb University of Edinburgh -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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EBI SRA for local galaxy
by Sergei Manakov 25 Mar '13

25 Mar '13

Hello, There is a tool called "EBI SRA" on public galaxy https://main.g2.bx.psu.edu/ I was wondering if there is a way to add it to my local instance of galaxy. I tried searching through the tool shed http://toolshed.g2.bx.psu.edu/ but I didn't find anything thanks, Sergei -- Sergei (Siarhei Manakou) Manakov California Institute of Technology MC 147-75 land: +1 626 395 3593 mobile: + 1 858 729 4531

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slow history panel?
by Langhorst, Brad 25 Mar '13

25 Mar '13

Is it my imagination or has the history panel become much slower in the latest release? Maybe I have something misconfigured? Brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com>

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Production Servers - Best Practices
by Rob Leclerc 25 Mar '13

25 Mar '13

I need a comprehensive understanding of the Best Practices for a Galaxy Production Server. (i) I've read "Running Galaxy in a Production Environment" and associated wikis (ii) I saw the presentations "Building Scalable Galaxy (2010)", "Deploying Galaxy on the Cloud (2010)", and "Cloudman: Galaxy on the Cloud". (iii) I've searched the mailing list. Are there any other *undocumented pitfalls/tips *that we should be aware of for a Cloudman/Amazon install? Security would be a high priority for this list. Below are a list of references I've compiled for my own list: Running Galaxy in a Production Environment<http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer> Sildes: Building Scalable Galaxy 2010<http://wiki.galaxyproject.org/Events/GDC2010?action=AttachFile&do=view&targ…> Deploying Galaxy on the Cloud, 2010<https://bytebucket.org/galaxy/galaxy-central/wiki/DevConf2010/galaxy_devcon…> Configure Apache Proxy to Galaxy<http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy> Configure nginx Proxy to Galaxy<http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy> Running Tests <http://wiki.galaxyproject.org/Admin/Running%20Tests> Presentation: CloudMan: Galaxy on the Cloud, 2011<http://vimeo.com/24870202> Cloudman Capacity Planning for AWS<http://wiki.galaxyproject.org/CloudMan/AWS/CapacityPlanning> Using Amazon EBS Volumes <http://aws.amazon.com/ebs/> Copying an Amazon EBS Snapshot<http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/ebs-copy-snapshot.html> ** Rob Leclerc, PhD <http://www.linkedin.com/in/robleclerc> <https://twitter.com/#!/robleclerc> P: (US) +1-(917)-873-3037 P: (Shanghai) +86-1-(861)-612-5469 Personal Email: rob.leclerc(a)aya.yale.edu

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Production and Dev server on the same database.
by Ted Goldstein 25 Mar '13

25 Mar '13

Hi Does anyone have any experience or advice about running two servers on the same database? The pros are that I can test tools and some other changes against actual datasets and check bug fixes directly by giving users temporary access to a dev server so that they regress the bugs themselves. The cons are that I risk damaging user data and ending up with a pile of rubble. I would like to have a production server and development server both running simultaneously. There are obvious issues such as the schema needs to be compatible for both systems simultaneously. This might mean disabling or enhancing the schema version control mechanism. What else needs to be modified to make this work? As the wicked witch of the west said "these things must be done very del-i-cate-ly" ;-) Thanks, Ted

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Boolean value issue with conditional tags
by Alexandre Loywick 25 Mar '13

25 Mar '13

Hi galaxians, I'm having an issue with tool parameters when using conditional tag and boolean parameters. My xml is like this: <conditional name="mis_allowed_conditional"> <param name="mis_allowed_bool" type="boolean" label="Allow mismatch ?" truevalue="-m" falsevalue="" checked="no"/> <when value="-m"> <param name="mis_allowed" type="float" value="0"/> </when> </conditional> and my command line is like: <command interpreter="python">wrapper.py $mis_allowed_conditional.mis_allowed_bool $mis_allowed_conditional.mis_allowed</command> The problem is when mis_allowed_bool isn't checked, I don't have any arguments in my command line (as expected). But, when it is checked, $mis_allowed_conditional.mis_allowed_bool is set to "True" and not to "-m". The strange thing is that the "mis_allowed" textfield is visible when mis_allowed_bool is checked so I guess that the when behaves as expected. Moreover, other boolean parameters that are not nested in a conditional work as they should. Is there something wrong with my xml or is this some kind of bug? Thank you for your answers, Alec

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user-specific tool panel
by Keilwagen, Jens 22 Mar '13

22 Mar '13

Hi guys, I'm wondering whether it is possible to have user-specific tool panels after logging in. This way users could customize the tool panel for instance by increasing the visibility of their (user-specific) favorites ... This would be a wonderful feature. However searching in the documentation and the mailing list, I did not find anything. Hence, it would be great if anybody could give me a hint or if impossible to mark this as a feature request. Thanks for any help. Jens

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