galaxy-user March 2010

galaxy-user@lists.galaxyproject.org

34 participants
35 discussions

SciPy 2010
by Glen Otero 30 Mar '10

30 Mar '10

Hello- If you're interested in presenting a tutorial or paper on Galaxy at the SciPy conference this year (http://conference.scipy.org/scipy2010/), I'd be very interested in hearing from you. The conference is being held in Austin, TX this year, and I am chairing the Bioinformatics track. It was at SciPy a few years ago that I first discovered Galaxy when James Taylor gave a presentation and I would really like to have a presentation in the Bio track this year that will update folks on all the progress Galaxy has made since then. Of course, I'd like to hear about all other Python-based bioinformatics projects too. Spread the word. It's going to be a great conference. Thanks! Glen

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BLAST
by Madison-Villar, Mercedita J 29 Mar '10

29 Mar '10

Hi... I have an analysis of 18,000,000 + sequences (X4) blasting through the HTGS database. Is there anyway to blast to a subset of this database to make the analysis much more speedy? Is the also a way to know if the analysis is working...ie periodic updates? I have had issues before with uploading large files where there is an error, but no error message. The data will look like its uploading when in fact it isnt. I just dont want to have to wait a week or weeks and find out the analysis is never going to end. Thanks!! Mersee Mersee Madison-Villar PhD Student, UT Arlington Lab/Office B01 Genomics, Speciation, and Evolutionary Biology "If evolution is outlawed, only outlaws will evolve"- Jello Biafra ________________________________________ From: galaxy-user-bounces(a)lists.bx.psu.edu [galaxy-user-bounces(a)lists.bx.psu.edu] On Behalf Of Guruprasad Ananda [gua110(a)bx.psu.edu] Sent: Monday, March 29, 2010 9:46 AM To: Andigoni Malousi Cc: galaxy-user(a)bx.psu.edu Subject: Re: [galaxy-user] problem report!! Hi Andigoni, I'm unable to reproduce the issue reported by you. I used the BED file sent by you as attachment and fetched sequences on it. The sequences produced were of the same lengths as in the BED file. Also, I computed summary statistics for the lengths of your BED intervals - the mean and median lengths were 19790 bp and 3466 bp respectively. Since you mention that you expect the constitutive exons to be 100-200 bp long, I'm guessing there might be a problem in one of the steps prior to the subtraction step in your pipeline. If you can share your history with me (guru(a)psu.edu<mailto:guru@psu.edu>), I can take a look at what might be going on. Here's how to do it: -go to the Options menu above your current history, select "Saved Histories" -go to the pull-down menu for the problematic history and select "Share or Publish" -share the history with me by clicking on "share with a user" and entering my email address: guru(a)psu.edu<mailto:guru@psu.edu>. Thanks for using Galaxy, Guru Galaxy team. On Mar 27, 2010, at 5:06 AM, Andigoni Malousi wrote: Dear Galaxy member, I'm sending you this e-mail because of a problem I have in fetching sequences. I used Galaxy to fetch sequences corresponding to alternatively spliced exons as well as constitutive exons. Here they are the steps I followed to do that: First, I extracted the coordinates of the ref genes from whole human genome: 1. I selected Get Data -> UCSC table browser 2. Genome: "Human", assembly: "Feb. 2009", Group: "Genes and Gene Prediction Tracks", Track:"RefSeq genes". 3. Filter: (+) region: Genome 4. "get output" and "Exons plus 0 bases…" Second, I extracted the coordinates of alternative splicing events 1. I selected "Get Data" -> "UCSC Main table browser". 2. Genome: "Human", assembly: "Feb. 2009", Group: "Genes and Gene Prediction Tracks", Track:"Alt Events". 3. Filter: (+) region: Genome Then, I stored the outcome of these two processes in BED format. To extract the coordinates of the constitutive exons I used the Subtract operation in "Operate on Genomic Intervals" 1. Substract: Alternative splicing events From: Ref genes 2. "Intervals with no overlap" 3. Stored the constitutive exon coordinates in BED format

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problem report!!
by Andigoni Malousi 29 Mar '10

29 Mar '10

Dear Galaxy member, I'm sending you this e-mail because of a problem I have in fetching sequences. I used Galaxy to fetch sequences corresponding to alternatively spliced exons as well as constitutive exons. Here they are the steps I followed to do that: First, I extracted the coordinates of the ref genes from whole human genome: 1. I selected Get Data -> UCSC table browser 2. Genome: "Human", assembly: "Feb. 2009", Group: "Genes and Gene Prediction Tracks", Track:"RefSeq genes". 3. Filter: (+) region: Genome 4. "get output" and "Exons plus 0 bases..." Second, I extracted the coordinates of alternative splicing events 1. I selected "Get Data" -> "UCSC Main table browser". 2. Genome: "Human", assembly: "Feb. 2009", Group: "Genes and Gene Prediction Tracks", Track:"Alt Events". 3. Filter: (+) region: Genome Then, I stored the outcome of these two processes in BED format. To extract the coordinates of the constitutive exons I used the Subtract operation in "Operate on Genomic Intervals" 1. Substract: Alternative splicing events From: Ref genes 2. "Intervals with no overlap" 3. Stored the constitutive exon coordinates in BED format Finally, using the "Fetch sequences" I tried to extract the genomic sequences for the outcome of the substraction (constitutive exons) in FASTA format. Please see the attached files for the extracted coordinates and sample sequences corresponding to constitutive exons. The strange thing about the results is that while constitutive exons are on average 100-200nt length the extracted sequences are much more larger. I was wondering whether there is something wrong in the whole procedure or this is a bug of Galaxy that we need to report. Thank you very much in advance, Andigoni Andigoni Malousi Post-doc in Bioinformatics Aristotle University of Thessaloniki

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Wiki Addition: Site Map and Site Index
by Kelly Vincent 26 Mar '10

26 Mar '10

Everyone, Bitbucket (our code and wiki host) does not offer any way to search the wiki, so there are now two new pages to fill the void: SiteMap and SiteIndex. These are both generated automatically. The idea is that the pages should be generated by a script that is scheduled to run each night, but I'm still getting that going--in the meantime, I'll be running the script manually. SiteMap is a simple listing of all the pages found under the base wiki directory. You can get a pretty good idea what the page is about just by the name of it, which is all that's included in this list. You can see SiteMap at http://bitbucket.org/galaxy/galaxy-central/wiki/SiteMap. SiteIndex is more complicated. It is a traditional index, which means that (almost) every word that appears in the wiki is included with a list of the pages on which it appears following it. A stoplist was used to remove useless or meaningless words, but there is still some junk that has made it past this filter. The index involves multiple pages, divided up alphabetically. It's available at http://bitbucket.org/galaxy/galaxy-central/wiki/SiteIndex . Regards, Kelly

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filtering lastz output to *best* match only
by Brant Faircloth 26 Mar '10

26 Mar '10

Apologies in advance if this isn't the best place to ask the following: I've RTFM-d for lastz-1.02.00 but may have missed it - is there currently any way to filter output from a lastz run such that _only_ the best match is returned (i'm currently doing this externally, but that seems inefficient if there's an option to do so). thanks in advance, b < * ) (_ \\ _ ||

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FTP and command line access in Galaxy
by S Taylor 23 Mar '10

23 Mar '10

Hi, We'd like to set up our local Galaxy to be able to import data (fastq sequences) from an ftp site (with a username/password) into a user's account. Does Galaxy support FTP or would we have to write a wrapper script to do it via HTTP and use the standard data connection methods as described in http://bitbucket.org/galaxy/galaxy-central/wiki/DataSources? My next question is, are there any recommendations to make it possible to allow access to Galaxy imported and generated data to be processed outside of Galaxy e.g. via command line? I guess using sudo and cp is an option but I wondered if anyone had any more thoughts on this! Thanks for any advice, Steve

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brand link
by Erick Antezana 23 Mar '10

23 Mar '10

Hi, Is there a way to (re)define (probably in the universe_wsgi.ini) the URL where our users will end up after clicking on the "brand" link? brand = Private local mirror cheers, Erick

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uploading large files/repeat sequences
by Keith E. Giles 23 Mar '10

23 Mar '10

I am trying to see if there are known repeat sequences in my chip seq data set, which are not uniquely alignable, and therefore thrown out by the eland algorithim in the sorted.txt file. I understand those sequences are present in the export.txt file. I am trying to upload that file to galaxy, but have not been able to yet. Does anyone know the file size limitation? Does anyone know the best way to compress such a file to upload it? I tried to gzip it, but for some reason the gzipped file has a .gzip.tmp filename, and I'm not sure if galaxy can handle this. Also, if anyone has any other suggestions on how to analyze the repeated portion of a chip seq, I'd be greatly appreciated.

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gnuplot : recommended version?
by Erick Antezana 22 Mar '10

22 Mar '10

Hi, I was trying to use the boxplot tool (Graph/Display Data) from within our local Galaxy instance (just updated yesterday). I faced a couple of issues while trying to generate boxplots. I was wondering which gnuplot version is actually recommended? While working with gnuplot version "4.0 patchlevel 0", one of the error messages was: line 0: undefined variable: tmargin gnuplot> plot '/tools/galaxy/database/files/000/dataset_94.dat' using 1:7:11:12:9 with candlesticks lt 1 lw 1 title 'Quartiles' whiskerbars, '' using 1:8:8:8:8 with candlesticks lt -1 lw 2 title 'Medians', "< python -c \"for xval, yvals in [ ( fields[1 - 1], fields[13 - 1].split( ',' ) ) for fields in [ line.rstrip( '\\n\\r' ).split( '\\t' ) for line in open( '/tools/galaxy/database/files/000/dataset_94.dat' ) if not line.startswith( '#' ) ] if len( fields ) > max( 1 - 1, 13 - 1 ) ]: print '\\n'.join( [ '%s\\t%s' % ( xval, yval ) for yval in yvals if yval ] )\"" using 1:2 with points pt 29 title 'Outliers' ^ line 0: ';' expected this can be overcome this by deleting "tmargin" form the "boxplot.xml" file. The second error message: gnuplot> plot '/tools/galaxy/database/files/000/dataset_94.dat' using 1:7:11:12:9 with candlesticks lt 1 lw 1 title 'Quartiles' whiskerbars, '' using 1:8:8:8:8 with candlesticks lt -1 lw 2 title 'Medians', "< python -c \"for xval, yvals in [ ( fields[1 - 1], fields[13 - 1].split( ',' ) ) for fields in [ line.rstrip( '\\n\\r' ).split( '\\t' ) for line in open( '/tools/galaxy/database/files/000/dataset_94.dat' ) if not line.startswith( '#' ) ] if len( fields ) > max( 1 - 1, 13 - 1 ) ]: print '\\n'.join( [ '%s\\t%s' % ( xval, yval ) for yval in yvals if yval ] )\"" using 1:2 with points pt 29 title 'Outliers' ^ line 0: ';' expected Again, I just removed "whiskerbars" and I got my plot... After getting updated my gnuplot (version 4.4), those issues were solved but there was another one related to the fonts, message: "Could not find/open font when opening font "arial", using internal non-scalable font" This could also be "fixed" by setting explicitly the font in the boxplot.xml (according to what I was just told, arial is proprietary and in some linux systems could represent an issue...): For instance: set term png size ${graph_size} font "/usr/share/fonts/liberation/LiberationSans-Regular.ttf,12" anyway, is there any gnuplot version recommended? Could the boxplot.xml be fixed/adapted to cope with those issues? cheers, Erick

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Re: [galaxy-user] galaxy-user membership
by Kelly Vincent 19 Mar '10

19 Mar '10

Steve, I've looked into your membership (stephen.taylor(a)imm.ox.ac.uk), and everything looks totally normal, so your posts shouldn't require approval. This one came through without approval, and the last one that did require approval was March 16. Your emails from yesterday all came from ocms0070(a)herald.ox.ac.uk, which is not a member of the list and would require approval. So it's possible that there was a problem that has worked itself out by now. But if you see it happening again, try unsubscribing and resubscribing, and if that doesn't work, let me know. Regards, Kelly On Fri 19 Mar 2010, at 3:05 AM, Steve Taylor wrote: > Hi, > > I am a member of the galaxy user list but every message I send > recently requires moderator approval. I tried to sign up again but > got the message I was already a member. Please can you have a look > what is going on. > > Kind regards and thanks, > > Steve > ============================================ > Head of Computational Biology Research Group > Weatherall Institute of Molecular Medicine > University of Oxford > John Radcliffe Hospital > Headington > Oxford OX3 9DS > +44 1865 222640

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galaxy-user March 2010