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

Re: [galaxy-dev] [galaxy-user] Cuffdiff question about using an unspecified (?) database/build
by Robert Curtis Hendrickson 25 Aug '11

25 Aug '11

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 > -----Original Message----- > From: galaxy-user-bounces(a)lists.bx.psu.edu [mailto:galaxy-user- > bounces(a)lists.bx.psu.edu] On Behalf Of David K Crossman > Sent: Friday, August 19, 2011 11:10 AM > To: Jennifer Jackson > Cc: galaxy-user (galaxy-user(a)lists.bx.psu.edu) > Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) > database/build > > Jen, > > Thank you very much for the reply. I'm glad to know it is a known bug > and not something on my side of things. So, would my analysis be affected if > I did change the bam file "Database/Build" to the older tree shrew version > found in the drop down list? What significance does this "Database/Build" box > have in downstream analysis if you have your own fasta reference genome file > and gtf annotation file that is being referenced instead of a locally cached > one? I'm just trying to obtain a better understanding of the "Database/Build" > box for analyses where I provide the fasta and gtf file. > > Thanks, > David > > > -----Original Message----- > From: Jennifer Jackson [mailto:jen@bx.psu.edu] > Sent: Friday, August 19, 2011 9:20 AM > To: David K Crossman > Cc: galaxy-user (galaxy-user(a)lists.bx.psu.edu) > Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) > database/build > > Hello David, > > This is a known bug. The correction is planned to be moved out onto the public > Galaxy instance at the next update (within a week). > > Sorry for the current inconvenience, > > Best, > > Jen > Galaxy team > > On 8/19/11 7:00 AM, David K Crossman wrote: > > Hello! > > > > I have an RNA-Seq project which consists of 5 samples from the species > > tree shrew. When uploading these fastq files into Galaxy, I chose > > "unspecified (?)" for the database/build since the latest tree shrew > > version is not in the drop down list. When using TopHat, > > Cufflinks/Compare I have selected a reference genome from my history > > instead of using a built-in index, as well as a gtf annotation file > > for Cufflinks/Compare and everything has been working fine. Now, I am > > at the Cuffdiff step and I am running into an error when setting it up > > to perform replicate analysis. When I select my TopHat accepted hits > > bam file I see a red X and the error: "Unspecified genome build, click > > the pencil icon in the history item to set the genome build." Here's a > > screenshot of what I'm seeing: > > > > Since the latest reference genome for tree shrew wasn't listed, that's > > why I chose "unspecified (?)." Should I go back and edit these > > accepted hits bam files to say the Database/Build from the drop down > > list is "Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1)?" I know that > > this is simple to change, but will this affect my results in any way? > > Any help/info would be greatly appreciated. > > > > Thanks, > > > > David > > > > > > > > ___________________________________________________________ > > 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/ > > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org/Support > > ___________________________________________________________ > 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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Galaxy public instances: data and job quotas
by Jennifer Jackson 25 Aug '11

25 Aug '11

Galaxy public instances: data and job quotas User data and job quota limits are now implemented at the public Galaxy Test instance http://test.g2.bx.psu.edu: http://galaxyproject.org/Test#Quotas While no quotas are currently implemented at the public Galaxy Main instance http://usegalaxy.org, we do ask that users stay within certain usage limits: http://galaxyproject.org/Main#Quotas If you find that you require additional resources, please consider the alternative Galaxy options explained at: http://galaxyproject.org/Big%20Picture/Choices Thanks for using Galaxy!

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Error when using build_profile_indexes.py on hg19
by Sarah Diehl 25 Aug '11

25 Aug '11

Hi everybody, when I run the build_profile_indexes.py script in the scripts/tools/annotation_profiler/ directory on hg19 (downloaded yesterday from UCSC), I get the following error: Created table dir (profiled_annotations/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal). ['fileName'] Table wgEncodeOpenChromFaireGlioblaBaseOverlapSignal (/galaxy/galaxy_data/ucsc_data/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal.sql) does not appear to have a chromosome, a start, or a stop. Removing empty table (wgEncodeOpenChromFaireGlioblaBaseOverlapSignal) directory (profiled_annotations/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal). Created table dir (profiled_annotations/hg19/wgEncodeCshlShortRnaSeqK562ChromatinShortTransfrags). ['bin', 'chrom', 'chromStart', 'chromEnd', 'name', 'score', 'strand', 'length', 'numUnique', 'numReads', 'minSeqCount', 'maxSeqCount', 'aveSeqCount', 'firstSeqCount', 'medSeqCount', 'thirdSeqCount', 'minReadCount', 'maxReadCount', 'aveReadCount', 'firstReadCount', 'medReadCount', 'thirdReadCount', 'numRegions', 'regStart', 'regLength', 'seqCount', 'regCount', 'sumCount', 'KEY', 'KEY'] Traceback (most recent call last): File "/galaxy/galaxy_backup/galaxy-dist/scripts/tools/annotation_profiler/build_profile_indexes.py", line 338, in <module> if __name__ == "__main__": __main__() File "/galaxy/galaxy_backup/galaxy-dist/scripts/tools/annotation_profiler/build_profile_indexes.py", line 310, in __main__ bitset_dict[ chrom ].set_range( start, end - start ) File "bitset.pyx", line 128, in bx.bitset.BitSet.set_range (lib/bx/bitset.c:1130) File "bitset.pyx", line 93, in bx.bitset.b_check_range_count (lib/bx/bitset.c:656) IndexError: End 16573 is larger than the size of this BitSet (16571). Everything worked fine with mm9 and dm3. Since the script wasn't changed in the last year, I suspect it has to do with the UCSC data. We don't really use hg19, so I'm fine with just leaving it out for now, but I wanted to report the error anyway. Best regards, Sarah

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creating new input/output formats
by Nikhil Joshi 25 Aug '11

25 Aug '11

Hi all, Is there a relatively easy way to create your own input/output formats? Some of the formats from programs that I am trying to install on our local Galaxy do not exist as an option. Any ideas? - Nik.

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Offering a user-paid NGS analysis pipeline in the cloud
by Sven-Eric Schelhorn 25 Aug '11

25 Aug '11

Dear Community, our lab has developed a NGS analysis pipeline for viral sequence analysis (both genomic resequencing and RNA-Seq, including some novel pathogen detection and viral quasi-species reconstruction approaches) that fulfills various analytical needs of our clinical cooperation partners. Since we believe that the pipeline might be of interest to the broader virological community we decided to integrate our workflow into Galaxy as a set of plugins. However, we do need our in-house computational capacities for our own analyses and are targeting people who do not have time and experience to set up their own Galaxy installation (for example, clinical virologists). Therefore, we would like to provide the finished product as a non-profit service in the cloud (for example, by using Amazon AWS, for which the Galaxy installation is pretty straightforward). We envision (or at least, hope) that the pipeline will be used heavily and would therefore like to transfer the costs for the used resources to the user (e.g., the clinical virologist) in a pay-as-you-go manner. Amazon offers its 'DevPay' service for these purpose, basically an infrastructure to bill users of an AWS application instead of the application provider. Again, we do not want to make any profit with this service, we just want people to pay for the cpu cycles they burn with as few hassles for us as possible. I could well imagine that other academic institutions have similar goals, e.g. being willing to offer their work for free without wanting to cover the costs for analysis resources. Does anyone have experience with similar kinds of setups and would like to offer advice? I am looking for hints about technical (e.g. how to best integrate a Cloud Galaxy with DevPay or similar) as well as legal hurdles that we might have to be careful about (e.g., are we in conflict with Open-Source Software Licenses if billing is involved, even if we do not make a profit etc.). Thanks a bunch! Grüße/Regards Sven-Eric Schelhorn -- Sven-Eric Schelhorn - http://mpi-inf.mpg.de/~sven Max Planck Institute for Informatics, Saarbrücken D3 - Computational Biology & Applied Algorithmics

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Issue with file permissions of uploaded files
by Joern Toedling 25 Aug '11

25 Aug '11

Hi all, we have our own Galaxy server running under Nginx. Recently we changed the 'user' of Nginx in the Nginx configuration file from 'galaxy' to a more general 'www' since we plan to use Nginx for other purposes as well. Now the "Get data -> Upload file" does not work any longer because of file permissions. Files are uploaded correctly to a directory /local/data/galaxy_tmp/upload_store/ but then are owned by the 'www' user and read-writeable by this other only. Thus, the Galaxy user 'galaxy' cannot open them, cannot determine the file type and the whole "Upload file" process fails. How can I set the file permissions of uploaded files? Do I need to enter a matching 'umask' in some Galaxy configuration or in some Nginx configuration file. Any links to where to set such a umask would be greatly appreciated. Thanks, Joern -- Joern Toedling, PhD Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de Tel.: +49 6131 39 21511

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checkboxes bug fix
by Louise-Amélie Schmitt 25 Aug '11

25 Aug '11

Hi, Since I haven't updated Galaxy for a while now I don't know if it was actually fixed but I had issues with my default-selected checkboxes: When I deselected them, the value sent in the query remained as if they were still selected. Even when I re-ran the job, all the checkboxes were selected as if I never deselected them. Therefore, in lib/galaxy/web/form_builder.py I changed: 105 return '<input type="checkbox" id="%s" name="%s" value="true"%s%s><input type="hidden" name="%s%s" value="true"%s>' \ for: 105 return '<input type="checkbox" id="%s" name="%s" value="true"%s%s><input type="hidden" name="%s%s" value="false"%s>' \ And it works fine now :) Cheers, L-A

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Re: [galaxy-dev] Installing local instance hiccup
by Kanwei Li 24 Aug '11

24 Aug '11

Ah, unfortunately we don't have a machine running Lion that can build the bundled eggs. Any chance you could change it to 2.6? "man python" in the command line should give instructions. For 10.6, the command is "defaults write com.apple.versioner.python Version 2.6" On Wed, Aug 24, 2011 at 6:20 PM, Stephen Doyle <S.Doyle(a)latrobe.edu.au>wrote: > Hi Kanwei, > > That would certainly help. Its a new MacBook Pro running OSX 10.7.1 and > Lion. > > Cheers, > Steve > > > > > > --------------------------------- > Dr Stephen R. Doyle > Postdoctoral Researcher > Genetics Department | La Trobe University | Bundoora 3086 > Australia > T: +61 3 9479 3087 | F: +61 3 9479 2480 | E: s.doyle(a)latrobe.edu.au | W: > http://www.latrobe.edu.au/genetics/staff/stephen_doyle.htm > > *La Trobe University - ranked top in Victoria for student satisfaction > (Sweeney Uni Student Report, 2009) > * > CRICOS Provider 00115M > > J Please kindly consider your environment before printing this e-mail > > Warning to recipients: > This email and any attachments are confidential and subject to copyright. > If you are not the intended recipient any use, disclosure or copying is > unauthorised. If you have received this email in error please advise us > immediately by reply email and delete all copies. It is your responsibility > to examine this email and any attachments for viruses. Any personal > information in this email must be handled in accordance with the Information > Privacy Act 2000 (Vic). > > > > > On 25/08/2011, at 1:33 AM, Kanwei Li wrote: > > Hi Stephen, > > What platform are you running on? > > Thanks, > > K > > On Wed, Aug 24, 2011 at 3:53 AM, Stephen Doyle <S.Doyle(a)latrobe.edu.au>wrote: > >> Hello, >> >> I am in the process of installing a local instance, and I can't seem to be >> able to build the bx_python egg, even with scramble.py. Any ideas to get >> around this? >> >> Cheers, >> Steve >> >> >> >> >> >> --------------------------------- >> Dr Stephen R. Doyle >> Postdoctoral Researcher >> Genetics Department | La Trobe University | Bundoora 3086 >> Australia >> T: +61 3 9479 3087 | F: +61 3 9479 2480 | E: s.doyle(a)latrobe.edu.au | >> W: http://www.latrobe.edu.au/genetics/staff/stephen_doyle.htm >> >> *La Trobe University - ranked top in Victoria for student satisfaction >> (Sweeney Uni Student Report, 2009) >> * >> CRICOS Provider 00115M >> >> J Please kindly consider your environment before printing this e-mail >> >> Warning to recipients: >> This email and any attachments are confidential and subject to copyright. >> If you are not the intended recipient any use, disclosure or copying is >> unauthorised. If you have received this email in error please advise us >> immediately by reply email and delete all copies. It is your responsibility >> to examine this email and any attachments for viruses. Any personal >> information in this email must be handled in accordance with the Information >> Privacy Act 2000 (Vic). >> >> >> >> >> >> ___________________________________________________________ >> 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/ >> > > >

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Sam2interval.py bug
by SHAUN WEBB 24 Aug '11

24 Aug '11

Hi, I've noticed a bug in sam2interval.py. There are a few indentation errors in the final lines of code. I think there should be an indent after: if not ref_name == '*': And this whole if statement should be included in the for loop above. Also, would you be able to add read_name to the truncated output (when not printing all fields). This makes downstream analysis a lot easier, e.g. looking at reads that map multiple times. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Re: [galaxy-dev] Failure to prepare job error
by Woozy 24 Aug '11

24 Aug '11

Hello, I'm running a Python/R tool from my Amazon Galaxy instance. To use R, I import a package I've installed called PypeR. My tool works fine from the command line, but when I try to run it on my Amazon instance, it gives me this error: Traceback (most recent call last): File "/nfs/software/galaxy/lib/galaxy/jobs/runners/local.py", line 61, in run_job job_wrapper.prepare() File "/nfs/software/galaxy/lib/galaxy/jobs/__init__.py", line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/nfs/software/galaxy/lib/galaxy/tools/__init__.py", line 1543, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/nfs/software/galaxy/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/nfs/software/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-i686-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1311891781_86_41894.py", line 83, in respond EOFError: EOF when reading a line With the additional caption "failure to prepare job". I've been struggling with this for days, and I'm pretty sure I don't have a typo in my .xml file. How can I solve this? Thanks, Rafi Torsten Schwab Marketing GmbH Emanuelstr. 3, 10317 Berlin Deutschland Telefon: +49 (33) 5310967 Email: woozydude(a)gmail.com Site: http://flug.prexxis.de/

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