galaxy-dev November 2011

galaxy-dev@lists.galaxyproject.org

83 participants
157 discussions

Re: [galaxy-dev] [galaxy-user] Upload executable in galaxy
by Nate Coraor 05 Dec '11

05 Dec '11

On Nov 23, 2011, at 11:10 AM, Giota Kottara wrote: > Dear galaxy developers, > > I am trying to integrate an executable tool in a private instance of galaxy. I stored the configuration .xml file and the executable in tools folder of Galaxy and the tool appears in the homepage. Nevertheless when i am running the tool it doesn't seem to find the executable. Am I forgetting something? Hi Giota, I've moved this over to the galaxy-dev list since it pertains to tool development. Executables will need to be on the $PATH of the user running Galaxy. Could you share the error messages you receive when you run the tool? --nate > > Thank you in advance > Giota Kottara > ___________________________________________________________ > 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/

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proxy settings?
by Smithies, Russell 04 Dec '11

04 Dec '11

I'm new to Galaxy so I'm not sure if this a Galaxy or linux/apache question . When I try to "Get Data" from UCSC or any other external site, I get a 407 error from our proxy as I need to authenticate. Is the request going out as the 'galaxy' user or 'apache' or the user that's logged in? I already have http_proxy and ftp_proxy configured in /etc/profile (we're running Centos 6) but I assume there a correct place to configure this for Galaxy? The error message I'm seeing is: An error occurred running this job: The remote data source application may be off line, please try again later. Error: ('http error', 407, 'Proxy Access Denied', <httplib.HTTPMessage instance at 0x35d2998>) Any ideas? Thanx, Russell Smithies ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

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Re: [galaxy-dev] GalaxyCloudman + CADDSuite
by Greg Von Kuster 02 Dec '11

02 Dec '11

Hello Marcel, In the future, please send all questions like this to the galaxy-dev mailing list, as doing so will streamline the process of getting a timely answer. I believe Enis is best able to answer your questions. Thanks! On Nov 30, 2011, at 9:29 AM, Marcel Schumann wrote: > Hi Greg, > > I'm currently trying to create a GalaxyCloudman version that includes CADDSuite. > Thus, I launched GalaxyCloudman as described in your wiki and tried to modify it afterwards. > > Well, starting cloudman worked without any problems... so far, so good :-) > As described on > http://wiki.g2.bx.psu.edu/Admin/Cloud/Customize%20Galaxy%20Cloud > I could then log-in via ssh as user 'ubuntu' (not as user 'galaxy'). > However, all files of the galaxy installation belong to user and group 'galaxy'. > > Thus my question: How should users be able to customize cloudman? Is there some trick by which I can log-in as 'galaxy' or do you have any other idea how to make this work ? ;-) > > Sorry Greg, if you are not the correct contact in this case, but I found not specific contact or mailing list for cloudman. Perhaps, you could just forward this mail in that case ... > > > Cheers, > Marcel > > > -- > Marcel Schumann > > University of Tuebingen > Wilhelm Schickard Institute for Computer Science > Division for Applied Bioinformatics > Room C313, Sand 14, D-72076 Tuebingen > > phone: +49 (0)7071-29 70437 > fax: +49 (0)7071-29 5152 > email: schumann(a)informatik.uni-tuebingen.de Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Job output not returned from cluster
by Joseph Hargitai 02 Dec '11

02 Dec '11

Hi, i was browsing through the list and found many entries for this issue but not a definite answer. We are actually running into this error for simple file uploads from the internal filesystem. thanks, joe

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Re: [galaxy-dev] [galaxy-user] Using Galaxy Cloudman for a workshop
by Clare Sloggett 01 Dec '11

01 Dec '11

Hi Jeremy, Enis, That makes sense. I know I can configure how many threads BWA uses in its wrapper, with bwa -t. But, is there somewhere that I need to tell Galaxy the corresponding information, ie that this command-line task will make use of up to 4 cores? Or, does this imply that there is always exactly one job per node? So if I have (for instance) a cluster made of 4-core nodes, and a single-threaded task (e.g. samtools), are the other 3 cores just going to waste or will the scheduler allocate multiple single-threaded jobs to one node? I've cc'd galaxy-dev instead of galaxy-user as I think the conversation has gone that way! Thanks again, Clare On Fri, Nov 18, 2011 at 2:36 PM, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote: > >> On Fri, Nov 18, 2011 at 12:56 AM, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote: >> >>> Scalability issues are more likely to arise on the back end than the front end, so you'll want to ensure that you have enough compute nodes. BWA uses four nodes by default--Enis, does the cloud config change this parameter?--so you'll want 4x50 or 200 total nodes if you want everyone to be able to run a BWA job simultaneously. >>> >> >> Actually, one other question - this paragraph makes me realise that I >> don't really understand how Galaxy is distributing jobs. I had thought >> that each job would only use one node, and in some cases take >> advantage of multiple cores within that node. I'm taking a "node" to >> be a set of cores with their own shared memory, so in this case a VM >> instance, is this right? If some types of jobs can be distributed over >> multiple nodes, can I configure, in Galaxy, how many nodes they should >> use? > > You're right -- my word choices were poor. Replace 'node' with 'core' in my paragraph to get an accurate suggestion for resources. > > Galaxy uses a job scheduler--SGE on the cloud--to distribute jobs to different cluster nodes. Jobs that require multiple cores typically run on a single node. Enis can chime in on whether CloudMan supports job submission over multiple nodes; this would require setup of an appropriate parallel environment and a tool that can make use of this environment. > > Good luck, > J. > > > > -- E: sloc(a)unimelb.edu.au P: 03 903 53357 M: 0414 854 759

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Lost my Data Libraries when I updated to the lastest galaxy-dist release?
by Liisa Koski 30 Nov '11

30 Nov '11

Hi, I lost my Data Libraries when I updated to the latest galaxy-dist release :( What would be the best way to go about getting them back? Thanks in advance, Liisa

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Local installation of the tool shed
by Nicolas Delhomme 30 Nov '11

30 Nov '11

Hi Greg, I've been scanning the mailing list, but wasn't lucky enough to find the answer I was looking for. Basically, we would be interested to have our own Galaxy Tool Shed in-house, to develop and test tools within our local Galaxy instance. What I'm thinking of, is to use the power of the tool shed to develop new algorithm, new tools, etc. that could be published afterwards. Because these would be sensitive material, we would not want to put them right away on the public test Tool Shed. Having a local Tool Shed instance would still be very helpful in releasing these tools to the community afterwards, as they would have been integrated and developed within that framework from the start. Any pointers on how to achieve this are welcome as I'm not so familiar with the Tool Shed yet, e.g. would making a local clone of the tool shed repository be enough? Thanks, Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme(a)embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany ---------------------------------------------------------------

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Re: [galaxy-dev] Toolshed not accessible
by Greg Von Kuster 30 Nov '11

30 Nov '11

You should not have to change things in your ini file if using the main Galaxy tool shed. On Nov 30, 2011, at 10:49 AM, Sajoscha Sauer wrote: > Now I'm confused :) > > I'm trying to use the Galaxy main toolshed (http://toolshed.g2.bx.psu.edu/), not a local one. I guess I don't have to change something in my ini file, right? > > We also updated to the revision 834de698004e > > Thanks, > Sajoscha > > On Nov 30, 2011, at 3:36 PM, Greg Von Kuster wrote: > >> I've recently added the following section to the tool shed wiki. Since you are using apache, make sure you have all of the necessary settings in community_wsgi.ini. Let me know if this is not the issue, and I'll need to see a complete paste log showing the exceptions as well as a copy of your community_wsgi.ini file. >> >> thanks, >> >> Greg Von Kuster >> >> http://wiki.g2.bx.psu.edu/Tool%20Shed#Hosting_your_own_local_tool_shed >> >> >> On Nov 30, 2011, at 7:22 AM, Sajoscha Sauer wrote: >> >>> Hi Greg, >>> >>> Sorry for the late reply! >>> >>> Yes, we see the error when trying to install a tool from the Galaxy tool sheds ('Install to local Galaxy') >>> >>> We are now back on yesterdays revision (3ee9430186fb) >>> >>> >>> Thanks, >>> Sajoscha >>> >>> On Nov 23, 2011, at 5:34 PM, Greg Von Kuster wrote: >>> >>>> Hi Sajoscha, >>>> >>>> What were you attempting to do when you saw this error? Are you still seeing this when you attempt to install a tool from the tool shed? By the way,m I just sent you an email - there are a few more fixes in the latest change set. >>>> >>>> >>>> On Nov 23, 2011, at 11:26 AM, Sajoscha Sauer wrote: >>>> >>>>> Hi Greg, >>>>> >>>>> Thanks for the quick response! >>>>> >>>>> We updated to the newest version from the Galaxy central repository, but still get the same error. But now there is a different error (or better, a different referer) in the apache log, see below. >>>>> >>>>> <Screen Shot 2011-11-23 at 5.11.19 PM.png> >>>>> >>>>> >>>>> >>>>> Thanks again for your help! >>>>> >>>>> >>>>> Sajoscha >>>>> >>>>> >>>>> On Nov 22, 2011, at 4:22 PM, Sajoscha Sauer wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> We are just about to enable the Toolshed on our development installation of Galaxy. >>>>>> >>>>>> We run the latest build (rev. b258de1e6cea) of Galaxy. >>>>>> >>>>>> >>>>>> The toolshed that we try to access is 'http://toolshed.g2.bx.psu.edu/' >>>>>> >>>>>> Our workflow is the following: >>>>>> - On the admin panel, click 'Search and browse tool sheds' >>>>>> - 'Browse valid repositories' on 'Galaxy main tool shed' >>>>>> - Select any tool and 'Preview and install' >>>>>> - 'Install to local Galaxy' >>>>>> >>>>>> >>>>>> What we see on the website is: >>>>>> >>>>>> <Screen Shot 2011-11-22 at 4.13.56 PM.png> >>>>>> >>>>>> The apache error log says: >>>>>> >>>>>> <Screen Shot 2011-11-22 at 4.06.34 PM.png> >>>>>> >>>>>> >>>>>> Any ideas and/or hints? >>>>>> >>>>>> >>>>>> Thanks a lot for your help! >>>>>> >>>>>> Sajoscha >>>>>> ___________________________________________________________ >>>>>> 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/ >>>>> >>>>> ___________________________________________________________ >>>>> 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/ >>>> >>>> Greg Von Kuster >>>> Galaxy Development Team >>>> greg(a)bx.psu.edu >>>> >>>> >>>> >>> >>> ___________________________________________________________ >>> 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/ >> >> Greg Von Kuster >> Galaxy Development Team >> greg(a)bx.psu.edu >> >> >> > Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Web links not leading to appropriate location anymore.
by Louise-Amélie Schmitt 30 Nov '11

30 Nov '11

Hello, We're experiencing a major issue in the web application and don't know where to look for a potential solution: Whichever link we click on it always brigs us back to the welcome page (galaxy/root). There are a few exceptions to that: - saved histories, saved datasets and api key in the User menu that lead to the appropriate pages - the tools on the left: even better, they open an new full set of Galaxy's frames in the middle frame. We tried reverting to the last pull, restarting Apache, checking the Apache config file, checking the rights in the static directory... and we still do not have the least idea of where to look. Does anyone have an idea, a lead to explore? Thanks, L-A

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Toolshed not accessible
by Sajoscha Sauer 30 Nov '11

30 Nov '11

Hi all, We are just about to enable the Toolshed on our development installation of Galaxy. We run the latest build (rev. b258de1e6cea) of Galaxy. The toolshed that we try to access is 'http://toolshed.g2.bx.psu.edu/' Our workflow is the following: - On the admin panel, click 'Search and browse tool sheds' - 'Browse valid repositories' on 'Galaxy main tool shed' - Select any tool and 'Preview and install' - 'Install to local Galaxy' What we see on the website is: The apache error log says: Any ideas and/or hints? Thanks a lot for your help! Sajoscha

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galaxy-dev November 2011