- galaxy-dev - lists.galaxyproject.org

Does Any Galaxy Format Converter Support Parallel Format Conversion?
by yi wang 29 Mar '12

29 Mar '12

Hi, Galaxy provides a couple of data format converters, but do they support format conversion in parallel? Where can I find the source code for these converters? Thanks, Yi Wang

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"AttributeError: 'NoneType' object has no attribute 'decode'" with Dataset Actions --> Select more datasets
by Leandro Hermida 29 Mar '12

29 Mar '12

Dear Galaxy Dev, On the viewed transferred datasets screen, when you click on Dataset Actions --> Select more datasets, I get the following error and stack trace: AttributeError: 'NoneType' object has no attribute 'decode' URL: http://galaxyserver/requests_admin/select_datasets_to_transfer?cntrller=req… Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:111 in __call__ view >> return self.app( environ, start_response ) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:145 in __call__ view >> body = method( trans, **kwargs ) Module galaxy.web.framework:139 in decorator view >> return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.requests_admin:355 in select_datasets_to_transfer view >> external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) ) Module galaxy.web.security:45 in decode_id view >> return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) AttributeError: 'NoneType' object has no attribute 'decode'

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"UnboundLocalError: local variable 'sample' referenced before assignment" when deleting transferred datasets
by Leandro Hermida 29 Mar '12

29 Mar '12

Dear Galaxy Dev, There seems to be another bug in the latest galaxy-dist, when you are on the Manage Datasets screen for a sample and you click on a few datasets that have been transferred and associated already and try select to delete them you get the following stack trace error: UnboundLocalError: local variable 'sample' referenced before assignment URL: http://galaxyserver/requests_admin/manage_datasets?sort=-create_time&show_i… Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:111 in __call__ view >> return self.app( environ, start_response ) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:145 in __call__ view >> body = method( trans, **kwargs ) Module galaxy.web.framework:139 in decorator view >> return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.requests_admin:239 in manage_datasets view >> sample_id=trans.security.encode_id( sample.id ), UnboundLocalError: local variable 'sample' referenced before assignment

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Re: [galaxy-dev] Error with mail in galaxy-dev mailing list
by Peter Cock 29 Mar '12

29 Mar '12

Hi Makis, Comments below... I have CC'd the galaxy-dev mailing list. 2012/3/29 Makis Ladoukakis <makis4ever(a)hotmail.com>: > Dear Peter, > > I am trying to send an e-mail inquiry in galaxy-dev mailing list but I keep > getting this error and my e-mail bounces back. Can you help me out please? > > Thank you in advance, > Makis Ladoukakis Have you also tried emailing galaxy-dev(a)lists.bx.psu.edu directly? You wouldn't normally use galaxy-dev-request(a)lists.bx.psu.edu > ... > > I am trying to format some BLAST databases to use with the BLAST+ tool > in a local Galaxy installation. According to this: > http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup > I have to use the blastdb command with some specific options in order to > generate the four necessary files (with extensions nhr, nin, nal, nsq). Are > these commands the same for both nucleotide and protein databases? Are these > files the same for both kinds of databases? First of all, the NCBI provides ready to use BLAST databases for NT, NR, etc on their FTP site: ftp://ftp.ncbi.nlm.nih.gov/blast/db/ The makeblastdb command is used to turn a FASTA file into a BLAST database (this is one of the BLAST+ command line tools). Use the argument -dbtype nucl or -dbtype prot (default) as appropriate. See the built in help for more: makeblastdb -help For nucleotide databases (which you tell Galaxy about using the blastdb.loc file) the extensions are nhr, nin, nsd, nsi, nsq plus also the special nal files for when a database is split into subparts (usually only done for very large databases like NT). For protein databases (which you tell Galaxy about using the blastdb_p.loc file) the extensions are phr, pin, psd, psi and psq plus also the special pal files for when a database is split into subparts (usually only done for very large databases like NR). Note that to refer to a BLAST database at the command line (or in Galaxy via blastdb.loc and blastdb_p.loc) you use the filename WITHOUT any extension. I hope that helps - you should consult the BLAST+ documentation for more background information like this. Regards, Peter

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toolrunner / xml parse
by Brami, Daniel 28 Mar '12

28 Mar '12

I am getting an error upon my local Galaxy startup which I suspect is causing an invalid tool runner entry in my left hand menu (my tool url is: http://localhost:8081/tool_runner/index instead of http://localhost:8081/tool_runner?tool_id=FLASHforFASTQ) Here is the error I get: galaxy.tools DEBUG 2012-03-28 13:48:28,658 Loading section: MyTools galaxy.tools DEBUG 2012-03-28 13:48:28,665 Loaded tool: sam_to_bam_QT 0.0.1 galaxy.tools DEBUG 2012-03-28 13:48:28,671 Loaded tool: BAMtoFASTQ 0.01 galaxy.tools.test DEBUG 2012-03-28 13:48:28,677 Error in add_param for readleft: Unable to determine parameter type of test input 'readleft'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2012-03-28 13:48:28,677 Error in add_param for readright: Unable to determine parameter type of test input 'readright'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools DEBUG 2012-03-28 13:48:28,678 Loaded tool: FLASHFASTQ 0.01 Here is the xml for my tool: <tool id="FLASHFASTQ" name="FLASH Overlap for FASTQ" version="0.01"> <description>Finds overlaps between paired fastq files or fills the insert with N's</description> <command interpreter="python"> FLASHforFASTQ.py --readleft=$readleft --readright=$readright --output=$output1 </command> <inputs> <data format="fastqsanger" name="readleft" type="data" label="Left fastq reads FASTQ files" ftype="fastqsanger" /> <data format="fastqsanger" name="readright" type="data" label="Right fastq reads FASTQ files" ftype="fastqsanger" /> </inputs> <outputs> <param format="fasta" name="output1" type="data" label="Overlap sequences in FASTA format"/> </outputs> <tests> <test>  <param name="readleft" value="quick-taxa.r1.fastq" type="data" ftype="fastqsanger" /> <param name="readright" value="quick-taxa.r2.fastq" type="data" ftype="fastqsanger" /> <output name="output1" file="quick-taxa.fasta" ftype="fasta" /> </test> </tests> <help> **What it does** This tool uses a modifed version of the FLASH overlapper to overlap paired end reads together and outputs the the resulting sequence in FASTA format </help> </tool> What's the problem?!?! Daniel Brami Synthetic Genomics, Inc. Senior Research Associate, Bioinformatics 11149 North Torrey Pines Road La Jolla, California 92037 Phone: 858.433.2230 Fax: 858.754.2988 DBrami(a)SyntheticGenomics.com<mailto:DBrami@SyntheticGenomics.com> www.SyntheticGenomics.com<http://www.syntheticgenomics.com/>

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Custom Get Data page doesn't recognize completion of large file downloads
by Brian Luerman 28 Mar '12

28 Mar '12

I have a custom module/page created to get data from some SOAP-based web services. I haven't determined the threshold yet, but for small BAM files, Galaxy behaves just fine. However, when I get large BAM files (I've had the same results with 10gig and 40gig files), Galaxy doesn't recognize when the download is complete. I can look in the /database/files/000 directory and see the download is complete (md5sum confirms it), but Galaxy just keeps on saying "Job is currently running". It takes a Galaxy reboot for it to recognize the complete download. Any ideas on how to fix this? Thanks -Brian

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add a tool to galaxy
by cai cai 28 Mar '12

28 Mar '12

Hi All, I am trying to add a tool to Galaxy, here is my xml configuration: ## Set params based on whether reads are single-end or paired. #if $singleOrPair.readType == "paired": --no_overlap $singleOrPair.readType.no_overlap #end if <conditional name="singleOrPair"> <param name="readType" type="select" label="single end or paired end reads"> <option value="single">single end</option> <option value="paired">paired end</option> </param> <when value="paired"> <param name="no_overlap" type="select" label=""> <option value="no">no</option> <option value="yes">yes</option> </param> </when> <when value="single" /> </conditional> I met the following error. Could some let me know what is wrong? Thank you very much. Cai Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", line 124, in queue_job job_wrapper.prepare() File "/mnt/galaxyTools/galaxy-central/lib/galaxy/jobs/__init__.py", line 372, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1585, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1332953248_1_41760.py", line 96, in respond*NotFound: cannot find 'no_overlap' while searching for 'singleOrPair.readType.no_overlap'*

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cluster_files_directory not getting cleaned
by Ann Black 28 Mar '12

28 Mar '12

Hello - I have noticed on our local install, that the job scripts as well as stdout/err in our cluster_files_directory is not getting cleaned up. When I track the jobs in our runner logs, for a sampling of the job scripts left over in the cluster_files_directory, the jobs are completing out successfully and there are no errors in the log. I have not tried to check if all scripts are not getting cleaned, or just some but by the volume of them it looks like all of them may not be getting removed/cleaned up after the job completes out. Any thoughts on what may be going on? Thanks, Ann

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Re: [galaxy-dev] [galaxy-user] Cleanup script error - guess_dialect_for_url
by Jennifer Jackson 28 Mar '12

28 Mar '12

Hi Rocco, To help us get oriented, which galaxy-dist pull did you start from and which did you update to? If you have the release date/hg pull numbers, that would be great. If you need to reference, these are the prior distributions: http://wiki.g2.bx.psu.edu/DevNewsBriefs Ideally, you would be current through the March 12, 2012 distribution, which included some bugs fixes for python 2.5 support. Support for python 2.4 ended with the Nov 18, 2011 distribution. If there is anything else customized about your system that you feel would be relevant (other odd behavior?), that would be good to send back. For example, can you delete and purge datasets through the UI? Histories? I am going to move your question over the galaxy-dev(a)bx.psu.edu mailing list, which is the best place to reach the development community. The galaxy-user list is intended for data/tool usage questions, with a focus on Galaxy main. http://wiki.g2.bx.psu.edu/Support#Mailing_Lists Please leave the galaxy-dev list in the "cc" for your return email, Thanks! Jen Galaxy team On 3/26/12 1:57 AM, rocco.piazza wrote: > Hello, > > I'm working on a local instance of Galaxy-dist and I just > updated it. Right after the update I tried to run the > cleanup scripts. Unfortunately what I'm getting is the > following error: > > # sh delete_datasets.sh -d 0 -r > Traceback (most recent call last): > File "./scripts/cleanup_datasets/cleanup_datasets.py", > line 524, in <module> > if __name__ == "__main__": main() > File "./scripts/cleanup_datasets/cleanup_datasets.py", > line 101, in main > app = CleanupDatasetsApplication( config ) > File "./scripts/cleanup_datasets/cleanup_datasets.py", > line 512, in __init__ > self.model = galaxy.model.mapping.init( > config.file_path, config.database_connection, > engine_options={}, create_tables=False, > object_store=self.object_store ) > File > "/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py", > line 1818, in init > load_egg_for_url( url ) > File > "/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py", > line 1798, in load_egg_for_url > dialect = guess_dialect_for_url( url ) > File > "/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py", > line 1794, in guess_dialect_for_url > return (url.split(':', 1))[0] > AttributeError: 'bool' object has no attribute 'split' > > The same error occurs if I try to run other cleanup > scripts, such as the delete_datasets or purge_datasets. > > Any idea to solve this issue? > > > Best regards, > Rocco > ___________________________________________________________ > 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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bug previewing data in new install
by Bartlett G Ailey 28 Mar '12

28 Mar '12

Hi, This is a new galaxy install and my initial test was downloading exon data from UCSC Main. The data failed to preview, I tried various alternatives and it seems to be related to the size of the data. Exon data from Chromosome 1-10 is displayed correctly while Chromosome 11-22 does not display any data at all. The small window does display the information. This is a strange error for a configuration mistake but I know the public server does not have the error so I have made a mistake somewhere. The log file does not display any errors though. Any suggestions on a solution or how to get more information on the error? Bart. PS Screen shots and paster.log information. Chromosome 10 preview working Description: cid:image001.png@01CD0CF7.76805630 Chromosome 11 preview not working Description: cid:image002.png@01CD0CF7.76805630 Log information from paster.log galaxy.web.controllers.dataset DEBUG 2012-03-28 15:22:48,488 Checking transfer status for dataset 25... 158.119.147.40 - - [28/Mar/2012:15:22:48 +0100] "GET /datasets/ba751ee0539fff04/transfer_status HTTP/1.1" 200 - "http://158.119.147.86:8080/history" "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.1) Gecko/20120225 Firefox/10.0.1" 158.119.147.40 - - [28/Mar/2012:15:22:48 +0100] "GET /datasets/ba751ee0539fff04/display/?preview=True HTTP/1.1" 200 - "http://158.119.147.86:8080/history" "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.1) Gecko/20120225 Firefox/10.0.1" galaxy.web.controllers.dataset DEBUG 2012-03-28 15:22:56,440 Checking transfer status for dataset 28... 158.119.147.40 - - [28/Mar/2012:15:22:56 +0100] "GET /datasets/a7db2fac67043c7e/transfer_status HTTP/1.1" 200 - "http://158.119.147.86:8080/history" "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.1) Gecko/20120225 Firefox/10.0.1" 158.119.147.40 - - [28/Mar/2012:15:22:56 +0100] "GET /datasets/a7db2fac67043c7e/display/?preview=True HTTP/1.1" 200 - "http://158.119.147.86:8080/history" "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.1) Gecko/20120225 Firefox/10.0.1"

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