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

Appending _task_%d suffix to multi files
by Alex.Khassapov＠csiro.au 07 Aug '13

07 Aug '13

Hi guys, We've been using Galaxy for a year now, we created our own Galaxy fork where we were making changes to adapt Galaxy to our requirements. As we need "multiple file dataset" - we were using Johns' fork for that initially. Now we are trying to use "The most updated version of the multiple file dataset stuff" https://bitbucket.org/msiappdev/galaxy-extras/ directly as we don't want to maintain our own version. One of the problems we have - when we upload multiple files - their file names are changed (_task_%d suffix is added to their names). On our branch we simply removed the code which does it, but now we wonder if it is possible to avoid this renaming somehow? I.e. make it configurable? Is it really necessary to change the file names? -Alex -----Original Message----- From: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Jorrit Boekel Sent: Thursday, 25 October 2012 8:35 PM To: Peter Cock Cc: galaxy-dev(a)lists.bx.psu.edu Subject: Re: [galaxy-dev] the multi job splitter I keep the files matched by keeping a _task_%d suffix to their names. So each task is matched with its correct counterpart with the same number. cheers, jorrit

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Blank History
by Alexander Kurze 07 Aug '13

07 Aug '13

Hi there, I am running my own instance of galaxy (April 2013 version) and I have problems with saved histories. Sometimes the histories do NOT show up at all at the right hand side (panel remains white with no error message). I then have make a clone of the history and then I can use it again. I haven't figured out what the problem could be. Does anyone have a similar problem? Best wishes, Alex

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Can I analyze *.csfasta & *.xsq data on Galaxy ?
by Nikhil Mallela 07 Aug '13

07 Aug '13

Hi, I am working on the colorspace data. I have one old data (*.csfasta, SOLiD4) & one new (*.xsq, 5500xl). I wanted to use tophat and cufflinks pipelines with Galaxy, Although tophat can make use of colorspace data, but galaxy seems to be accepting only FASTQ format for most of its tools. And the online community is strongly discouraging the conversion of colorspace to FASTQ. So, is there any work-around for this problem ? Do I have to modify the scripts according to my requirement in my local installation ? Looking forward for your advise. Thanks in advance, Nikhil. -- ------------------------------------------------------------ Nikhil Vinod Mallela, M.Sc. University of Muenster, Institute of Bioinformatics, Neil-Stensen Str. 12-14, 48149, Muenster,Germany. Tel.: +49 0251 83 50006 Fax: +49 0251 83 53005Email: mallela@uni-muenster.dehttp://complex-systems.uni-muenster.de/------------------------------------------------------------

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Galaxy -> IGV. Problem with bam and bai files
by Moritz Juchler 07 Aug '13

07 Aug '13

Hello Galaxy Team, I get this error > "Error reading bam file. This usually indicates a problem with the index > (bai) file. ArrayIndexOutofBoundsException: 6921 (6921)." when I finish my pipeline and try do view any of the sam or bam files. -occurs on both hg19 and hg_g1k_v37 -i tried to sort and index the sam file from step 22 and 25 in igv, but without success and ideally I do not want to have any steps outside Galaxy. -I get the error on the data of step 44, 38 and 35 Opening the sam file from step 25 gives: "could not find index" and after I use the tools in IGV it works and I can look at the aligned sequences, but still this is a step outside of Galaxy, which I do not want. Anything I overlooked? I'd appreciate every hint. Best Moritz

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Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
by Dave Bouvier 07 Aug '13

07 Aug '13

Rodolfo, Please keep the thread on the mailing list by using the "Reply all" option. You should now be able to go to the manage repository page, select the tool dependency, then select 'Manage tool dependencies' from the repository actions dropdown and reinstall the blast+ tool dependency. --Dave B. On 8/5/13 14:03:14.000, Rodolfo Aramayo wrote: > Dear Dave, > > Answers below... > > On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier <dave(a)bx.psu.edu> wrote: >> Rodolfo, >> >> In order to simplify tracking down this issue, could you provide the >> changeset revision of Galaxy that is running on tamu.edu? To retrieve the >> revision, execute the following command in your galaxy root directory: >> >> hg id > > fd4113962c32+ (stable) > >> >> To clarify, our understanding is that you installed the ncbi_blast_plus >> repository from the main tool shed, and it installed correctly. You then >> uninstalled the repository, and it also uninstalled properly. You then >> attempted to reinstall the repository, and encountered the error message >> cited in your email. >> >> Can you confirm the above? > > This is correct > >> >> We further understand that the repository is stuck in the 'installing' >> state. > > YES and in the "Manage installed tool shed repositories" says now > (after having to restart Galaxy for another reason): > > "Installed, Missing tool dependencies" > > > What options are available from the popup menu next to the >> ncbi_blast_plus repository on the manage installed repositories page? > > If I click on the little arrow, it says: > > Get updates > Deactivate or uninstall > >> 'Deactivate or uninstall' is available, can you try uninstalling again, and >> see if that functions correctly? > > It worked! > > Before I was not able to do it as I was getting an ugly galaxy error page > But now it did uninstall and removed and was able to clone correctly. > However, the directory: > > ./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/ > > is empty! > > > Should I repopulate it with the one I have in my backup?? > > Thanks > > --Rodolfo > > >> >> --Dave B. >> >> >> On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote: >>> >>> People, >>> >>> I successfully installed NCBI_Blast_Plus from the toolshed >>> The tool, however, failed to work giving the following error: >>> >>> Fatal error: Exit code 255 () >>> Error: NCBI C++ Exception: >>> >>> "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", >>> line 689: Critical: ncbi::CObject::ThrowNullPointerException() - >>> Attempt to access NULL pointer. >>> >>> I then tried uninstalling/reinstalling the tool >>> >>> However I now get an eternal 'installing' grey message and when I >>> click 'manage the repo' I get: >>> >>> ######### >>> >>> URL: >>> http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e1499… >>> File >>> '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', >>> line 149 in __call__ >>> app_iter = self.application(environ, sr_checker) >>> File >>> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', >>> line 84 in __call__ >>> return self.application(environ, start_response) >>> File >>> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', >>> line 633 in __call__ >>> return self.application(environ, start_response) >>> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', >>> line 132 in __call__ >>> return self.handle_request( environ, start_response ) >>> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', >>> line 190 in handle_request >>> body = method( trans, **kwargs ) >>> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', >>> line 221 in decorator >>> return func( self, trans, *args, **kwargs ) >>> File >>> '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', >>> line 561 in manage_repository >>> repository = suc.get_installed_tool_shed_repository( trans, >>> repository_id ) >>> File >>> '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py', >>> line 515 in get_installed_tool_shed_repository >>> return trans.sa_session.query( trans.model.ToolShedRepository ).get( >>> trans.security.decode_id( id ) ) >>> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py', >>> line 60 in decode_id >>> return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( >>> "!" ) ) >>> ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b' >>> >>> ######### >>> >>> How can I totally uninstall and re-install this tool? >>> >>> Thanks >>> ___________________________________________________________ >>> 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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UGENE tools integration into Galaxy web-platform
by Пётр Леонтьев 07 Aug '13

07 Aug '13

Hello, Galaxy team. I am writing you to find out the right way about how can be other bioinformatics tools integrated into your web-platform. I will explain more detail: we have in our bioinformatics software UGENE a tool "Workflow designer". It has different elements for simple sequences operations as well as MSA algorithms, NGS analysis and so on. You can create new scheme in the workflow designer, set parameters that will be shown at new Galaxy tool window and then just generate tool config file. In Galaxy you can run this tool and get results at history panel and use it futher (in other Galaxy tools). I attached simple scheme example and showed how to generate config for it. Also there is a picture of our scheme in Galaxy. Exact answer is very interesting for us and we will hope to hear good response. I will be grateful to you if this letter will be sent to correct address if that is not so. Kind Regards, Peter Leontev, UGENE team

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[galaxy-user] History & Visualization list empty
by Jennifer Jackson 07 Aug '13

07 Aug '13

Hello Ben, No graphics are included with the post, which isn't a great idea anyway on a mailing list. On 8/2/13 11:16 AM, Benjamin Schuster-Boeckler wrote: > Hi there, > > I've set up a local galaxy installation that so far is working very > nicely. However one little issue that I'm having is that the "Saved > Visualizations" and "Saved Histories" lists are empty, even though I > have multiple histories and multiple visualizations. In fact, when I > choose to visualize a dataset in Trackster and select "View in saved > visualization", I DO see the list of existing visualizations. Still, this is very strange. To get started, can you confirm that you are running the most current version of Galaxy? http://wiki.galaxyproject.org/DevNewsBriefs I am also going to move this over to the galaxy-dev(a)bx.psu.edu mailing list, the list for questions regarding local instances. So please be sure to send all replies "To" back the galaxy-dev mailing list, but please drop the galaxy-user list. We will probably need some technical help from the developers to get to the bottom of what is going on. Thanks, Jen Galaxy team > Pictures attached. The identical problem appears with Histories. Any > idea what the problem might be? I tried in Chrome and Safari, I logged > out and back in, I restarted the server, but nothing fixed the issue... > > Thanks in advance for the help, > Ben > > -- > Benjamin Schuster-Böckler > Leadership Fellow for Bioinformatics > > Ludwig Institute for Cancer Research > University of Oxford > Old Road Campus Research Building > Oxford OX3 7DQ > United Kingdom > > > ___________________________________________________________ > 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 http://galaxyproject.org

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Error running oasesoptimizer rev. 53e887dda799 (konradpaszkiewicz) on Galaxy fd4113962c32+ (stable)
by Rodolfo Aramayo 07 Aug '13

07 Aug '13

Attempting to run oasesoptimizer rev. 53e887dda799 (konradpaszkiewicz) on Galaxy fd4113962c32+ (stable) I get the following error: ##### error An error occurred with this dataset: Traceback (most recent call last): File "/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py", line 120, in if __name__ == "__main__": __main ##### Traceback (most recent call last): File "/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py", line 120, in <module> if __name__ == "__main__": __main__() File "/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py", line 69, in __main__ for line in open(transcript_path): IOError: [Errno 2] No such file or directory: 'transcripts.fa' ##### The input file is part of my history and it is in fastqsanger format I get the same error after converting fastqsanger to fasta format Ideas? Thanks --Rodolfo

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RFC: Implement 'cloudbiolinux_install' tool shed package install action.
by John Chilton 06 Aug '13

06 Aug '13

I have implemented a cool idea Brad Chapman had the recent BOSC Codefest. It would save me tons of effort related to maintaining separate proteomics module definitions for the tool shed and CloudBioLinux for Galaxy-P. I thought I would throw this out there and see if anyone has any comments: >From the pull request: CloudBioLinux contains custom fabric install procedures for dozens of bioinformatics packages and new ones are added all the time. It also contains code used to automatically setup Galaxy env.sh files to support multiple versions of given software. While it started off as a way to configure a particular distribution of Linux, it now supports many distributions and these custom install procedures in particular are not tied to any particular varaint of Linux or even Linux itself. This changeset adds the ability for Tool Shed tools to quickly and easily leverage this wealth of Galaxy module ready software. In particular it adds a new action type - 'cloudbiolinux_install'. I have created the repository 'ngscbltest' in 'Next Gen Mappers' section on the Test Tool Shed to demonstrate and test this functionality. Here is an example from 'tool_dependencies.xml' in that repository: <tool_dependency> <package name="tophat2" version="2.0.8b"> <install version="1.0"> <actions> <action type="cloudbiolinux_install" cbl_revision="4bd005355991a5c8b855ea790ae75e8178ede8c1" tool_name="tophat2" tool_version="2.0.8b" /> </actions> </install> <readme>Tophat 2.</readme> </package> ... </tool_dependency> When installed into a Galaxy instance, this example will cause the version '2.0.8b' to be passed to the 'install_tophat2' function in CloudBioLinux and configure it to install into the directory expected by the Tool Shed client code. Additonally, CloudBioLinux will setup an env.sh file for this installation. All of this will be installed as a 'tophat2' package. In the above example,a particulr revision of CloudBioLinux was specified for the sake of reproducibility. That attribute is optional however and will default to 'master'. Likewise, reasonble defaults for the attributes 'tool_name' and 'tool_version' can be inferred from context. As a demonstration, the following package definition would result in Tophat 1.3.3 being installed as the package 'tophat'. <package name="tophat" version="1.3.3"> <install version="1.0"> <actions> <action type="cloudbiolinux_install"/> </actions> </install> <readme>Tophat 1.3.3.</readme> </package> The name of install method doesn't have to match the packge name, for instance the install_cufflinks function in CloudBioLinux can be used to install Cufflinks 1 or 2 as shown below: <package name="cufflinks2" version="2.1.1"> <install version="1.0"> <actions> <action type="cloudbiolinux_install" cbl_url="https://github.com/jmchilton/cloudbiolinux.git" tool_name="cufflinks" /> </actions> </install> <readme>Cufflinks2.</readme> </package> This final example also demonstrates how to target a customized fork of CloudBioLinux. Implementation: On the Galaxy side of this equation, the implementation is fairly straight forward. fabric_util.py has been updated with a '__install_cloudbiolinux_tool' function which implements this action entirely. This function clones clodubiolinux to a temporary directory (optionally checking out a particular revision), and uses the CloudBioLinux deployer functionality to configure a local, no-ssh install of the specified software. Requirements: The core framework for obtaining and running CloudBioLinux requires only bash, wget, git, and python-dev/python-devel. These are likely a subset of packages the IUC has already agreed will need to be present. Individual install procedures may have additonal OS level requirements, but the same could be true of any Make file compiled with the existing Tool Shed infrastructure. If particular modules are isolated as being useful, I am happy to work with the tool developers to ensure the CloudBioLinux install procedure can work with minimal prerequisites. Thanks, -John

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Re: [galaxy-dev] Local installation: Questions about using rsync to retrieve a genome
by Gerald Bothe 06 Aug '13

06 Aug '13

I'll leave the rsync question to the experts - worked for me, but I don't know why it worked for me (linux/ubuntu laptop, not networked) and not for you . About the filenames: You can download a file listing to text.txt by .../galaxy-dist$ rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes > text.txt and then choose which one you want. File size warning: this is something like 200 MB. Trying to download the much shorter list for phiX might be a quick way to check whether it works: .../galaxy-dist$ rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX > phiXlist.txt Gerald >________________________________ > From: Boaz Shaanan <bshaanan(a)bgu.ac.il> >To: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> >Sent: Tuesday, August 6, 2013 4:25 PM >Subject: [galaxy-dev] Local installation: Questions about using rsync to retrieve a genome > > > > >Hi, > > >1) I'd like to fetch the genome of H. salinarum NRC-1 on my local installation. Following your advice (http://wiki.galaxyproject.org/Admin/Data%20Integration >I wanted to use rsync. To begin with I tried the example in the above url, even though that's not the genome I'm interested in: > > > rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX . > >I didn't get any response. My questions are: >1) Is it because the ftp site was not on ? Or could it be a firewall problem? Can the site be accessed in a different way that I can try? >2)Where can I find the file name where the H. salinarum NRC-1 genome resides on the server? > > > Thanks for your help. > > > Boaz > > >Boaz Shaanan, Ph.D. >Dept. of Life Sciences >Ben-Gurion University of the Negev >Beer-Sheva 84105 >Israel > >E-mail: bshaanan(a)bgu.ac.il >Phone: 972-8-647-2220 Skype: boaz.shaanan >Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > >___________________________________________________________ >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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