August 2011 - galaxy-dev - lists.galaxyproject.org

LDAP & NGINX
by Holger Klein 26 Aug '11

26 Aug '11

Dear all, I'd like to integrate external user authentication with our local galaxy installation. So far we are running nginx as proxy, but all examples I found for LDAP and galaxy are for apache. Is anybody out there who has a working installation with LDAP and nginx? Cheers, Holger -- Dr. Holger Klein Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de/ Tel: +49(6131) 39 21511

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Customizing/reusing the workflows/run.mako template
by Duddy, John 26 Aug '11

26 Aug '11

I'd like to integrate with Galaxy and launch workflows, and I am hoping to reuse Galaxy's support for prompting the user for items that are tagged as being set at runtime. It looks to me that I could load the workflows/run page in a frame on my app (on the same server) and reuse it. The problem I'm having is that I don't understand how the parameters for the input files are encoded. For example, here is one for adding a column to a dataset: <select name="22|input" last_selected_value="53"> <option value="53" selected>1: Add column on data 6</option> </select> <input type="hidden" name="22|__force_update__input" value="true" /> </div> <div style="clear: both"></div> </div> What are 22 and 53? They don't seem to correspond to dataset IDs. Is there a way that I can encode data library IDs such that I can submit this form and have Galaxy run the workflow with the right files in a new history? Thanks! John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com<mailto:jduddy@illumina.com>

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Re: [galaxy-dev] external display app
by Bram Slabbinck 26 Aug '11

26 Aug '11

Hi A small question regarding the setup of an external display application. At this moment, I have a display application that is linked to a particular datatype and everything shows up fine. In a second step, I want to make the visualisation more dynamic and therefore I need to have access to the input parameters of the tool that is used to create the particular data set. Is there a way to access these parameters from within my display application xml form? Maybe similar to the functionality of the info button of the dataset history item, which shows a list of all tool input parameters? I have looked at the according mako file and associated scripts, and the external display application wiki page but did not find a practical solution. As an alternative, I could put my tool parameters on top of my tool form and parse the value of the $data.info parameter (<param type="data">; column 'info' in the history_dataset_association table) within a <param type="template"> tag. This value shows however only the first x variables and, therefore, this approach is not a very decent way of parameter handling. thx for any suggestions Bram

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Metadata error
by Chorny, Ilya 26 Aug '11

26 Aug '11

I get these two error in the log file. The job finishes correctly and a metadata file is created but I still get the error. Can anyone provide me with more detail about what this error means? The second error is incorrect because the files were deleted. setting metadata externally failed for HistoryDatasetAssociation 344: [Errno 1] Operation not permitted: '/mnt/data/galaxy/database/files/000' and Failed to cleanup MetadataTempFile temp files from ../../mnt/data/galaxy/database/tmp/metadata_out_HistoryDatasetAssociation_344_NUDu3A: No JSON object could be decoded: line 1 column 0 (char 0) Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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What script updates the umask of database/files/* and deletes database/job_working_directory
by Chorny, Ilya 26 Aug '11

26 Aug '11

When running as the actual user in drama, I made it so the .dat files are not initially created so that when a tool moves data from the a temp directory to the out .dat file it will not fail. (i.e. unix does not allow moving a file owned by one user to a file owned by another user because mv carries the attributes of the original file). Now I want to change the ownership of the files through a sudo call at the end. Which script is run at the end to clean things up? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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Re: [galaxy-dev] [galaxy-user] Cuffdiff question about using an unspecified (?) database/build
by Jennifer Jackson 26 Aug '11

26 Aug '11

Hi Curtis, This is a good question. I'll post back to the list to (hopefully) gather some feedback. Thanks! Jen On 8/25/11 8:44 AM, Robert Curtis Hendrickson wrote: > Wonderful. We're on galaxy-dist, but we can pull that patch. > Are most local installs on Dist or Central? > > Thanks! > > Curtis > > > >> -----Original Message----- >> From: Jennifer Jackson [mailto:jen@bx.psu.edu] >> Sent: Thursday, August 25, 2011 10:41 AM >> To: Robert Curtis Hendrickson >> Cc: David K Crossman; 'galaxy-dev(a)lists.bx.psu.edu' >> Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) >> database/build >> >> Hi Curtis, >> >> Changeset details: >> http://bitbucket.org/galaxy/galaxy-central/changeset/07de40a5a0b9 >> >> We are planning on releasing a distribution within a week, so >> alternatively you could wait and pull from there, if you normally work >> from the galaxy-dist repository. >> >> And for everyone tracking this fix: the changeset was applied to the >> public Galaxy main instance yesterday (http://usegalaxy.org) >> >> Hope this helps! >> >> Jen >> Galaxy team >> >> On 8/25/11 7:55 AM, Robert Curtis Hendrickson wrote: >>> Jen, >>> >>> Can you also please describe the details of the fix? >>> We need to fix the same issue in our local instance, but don't know if this >> was a fix to cuffdiff, or to galaxy. Which one should we be updating? >>> >>> Regards, >>> Curtis -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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tool which using web service
by shashi shekhar 26 Aug '11

26 Aug '11

hi, I have application , i want to integrate that application like ucsc_browser in my local instance of galaxy .Application create some input data ,that data i want to send into galaxy to process. can u help me how can i add such type of tool in Galaxy ? Regards shashi

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can someone explain outputs of bowtie_wrapper.xml?
by Nikhil Joshi 25 Aug '11

25 Aug '11

Hi all, I am trying to figure out the meaning of the XML within the <outputs>...</outputs> portion of the bowtie_wrapper.xml file. The tool config syntax page doesn't really explain the details that well. Can someone point me to somewhere, or just explain, what is going on? For example, here is the outputs part of that file: <outputs> <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> <actions> <conditional name="refGenomeSource.genomeSource"> <when value="indexed"> <action type="metadata" name="dbkey"> <option type="from_data_table" name="bowtie_indexes" column="1" offset="0"> <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> <filter type="param_value" ref="refGenomeSource.index" column="0"/> </option> </action> </when> <when value="history"> <action type="metadata" name="dbkey"> <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> </action> </when> </conditional> </actions> </data> <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)"> <filter>(( singlePaired['sPaired'] == "single" and singlePaired['sParams']['sSettingsType'] == "full" and singlePaired['sParams']['sMaxFile'] is True ) or ( singlePaired['sPaired'] == "paired" and singlePaired['pParams']['pSettingsType'] == "full" and singlePaired['pParams']['pMaxFile'] is True )) </filter> <actions> <conditional name="singlePaired.sPaired"> <when value="single"> <action type="format"> <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> </action> </when> <when value="paired"> <action type="format"> <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> </action> </when> </conditional> </actions> </data> <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)"> <filter>singlePaired['sPaired'] == "paired"</filter> <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter> <filter>singlePaired['pParams']['pMaxFile'] is True</filter> <actions> <conditional name="singlePaired.sPaired"> <when value="single"> <action type="format"> <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> </action> </when> <when value="paired"> <action type="format"> <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> </action> </when> </conditional> </actions> </data> <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)"> <filter> (( singlePaired['sPaired'] == "single" and singlePaired['sParams']['sSettingsType'] == "full" and singlePaired['sParams']['sUnmappedFile'] is True ) or ( singlePaired['sPaired'] == "paired" and singlePaired['pParams']['pSettingsType'] == "full" and singlePaired['pParams']['pUnmappedFile'] is True )) </filter> <actions> <conditional name="singlePaired.sPaired"> <when value="single"> <action type="format"> <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> </action> </when> <when value="paired"> <action type="format"> <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> </action> </when> </conditional> </actions> </data> <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"> <filter>singlePaired['sPaired'] == "paired"</filter> <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter> <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter> <actions> <conditional name="singlePaired.sPaired"> <when value="single"> <action type="format"> <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> </action> </when> <when value="paired"> <action type="format"> <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> </action> </when> </conditional> </actions> </data> </outputs> It seems like each output has conditionals, some of which are setting DB keys, but with others I can't tell what is going on. For example, I can't find anything about a "type" or "name" or "param_attribute" value that you can set within the <option> tag, for example. Anybody know what those mean? Also, still can't really figure out what values are possible to set for the <action> tag. Any help would highly appreciated. Thanks! - Nik.

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Updated Cufflinks Wrapper
by Chorny, Ilya 25 Aug '11

25 Aug '11

I made some changes to the cufflinks wrapper. I added the -g/--GTF-guide use reference transcript annotation to guide assembly as an option. The version number needs to still be updated in my commit. https://bitbucket.org/ichorny/galaxy-central/changeset/fc5e24d453e5 Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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"filtering" BED files by score in trackster
by Hans-Rudolf Hotz 25 Aug '11

25 Aug '11

Hi The option to filter a BED file by the score in the visualization tool is brilliant! There is just one draw back: you can only filter by integers. Hence a score of 1.1 is the same as of score of 1.3. How difficult would it be to change the code in order to allow floats for the filter? Such a feature would help us a lot! I tried to dig into the visualization code...but I got lost. Thank you very much for your help Regards, Hans

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