- galaxy-dev - lists.galaxyproject.org

From workflow to script
by Victoria D Bohler 08 Aug '13

08 Aug '13

Hello, A naïve question, is it possible obtained from a galaxy-workflow a shell script?, if yes, how can I do it? Thank you in advance for your answer, Victoria

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Galaxy with LSF scheduler
by Auerbach, Kenneth R. 08 Aug '13

08 Aug '13

Hello, Can anyone tell me if there are detailed instructions anywhere for setting up Galaxy on a Linux cluster using an LSF scheduler? Thank you. Ken. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Oasesoptimiser Problem: Transcripts.fa not found
by Ricardo Perez 08 Aug '13

08 Aug '13

Dear all, When I try to run oasesoptimiser <https://galaxy.tamu.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos/ko…> in Galaxy I get the following error: 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' Anyone knows what is the source of this problem? Thank you for your time, --Ricardo Perez

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Map with BWA results in correpted SAM file
by Moritz Juchler 08 Aug '13

08 Aug '13

Dear Galaxy Community, I have a local instance and installed 0.5.9-r16 BWA and the toolshed wrapper. The mapping is successful. I then use the Filter Sam Tool on the sam file from the alignment, but it spits out this error: *Dataset 26: Filter SAM on data 24* Tool execution generated the following error message: Traceback (most recent call last): File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py", line 148, in <module> if __name__ == "__main__": main() File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py", line 137, in main flags = int( fields[flag_col] ) ValueError: invalid literal for int() with base 10: 'RG:Z:lane712s006433' I have the same workflow online and did the exact same steps on the same fastq files. Is there anything I am missing? Is there any information I can provide to answer this question? Best Moritz

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how to generate a workflow with customized tool names
by Jun Fan 08 Aug '13

08 Aug '13

Dear all, I have a tool which contains the function A,B, and C, the output of the function is the input of another function. I have developed a wrapper for this tool using conditional tag to allow users select the function they want. The label of the outputs (datasets) can be defined by label attribute in the outputs. So far so good. However, when I tried to create a workflow from history, the three steps (functions) from the tool are labeled with the same text (the title of the wrapper). My question is how to customize it, e.g. function_A_tool_name, function_B_tool_name which clearly tell the users which function is used instead of the need to check the parameter setting. Best regards! Dr Jun Fan Postdoctoral Researcher School of Biological and Chemical Sciences Queen Mary University of London

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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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