December 2009 - galaxy-user - lists.galaxyproject.org

Updating my Galaxy install
by Erick Antezana 21 Dec '09

21 Dec '09

Hi, I was wondering whether there is a wiki page on the http://bitbucket.org/galaxy/galaxy-central site where I could find some detailed information about updating my local install of Galaxy? so far I have been regularly updating it by using mercurial (hg pull -u) However, it seems that some files are not properly updated ... (like the data cleaning/purging scripts).. Am I missing something? thanks in advance, Erick

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purging deleted datasets
by Erick Antezana 17 Dec '09

17 Dec '09

Hi, how can I purge my deleted datasets that were imported so that I could clean a bit my disk? I saw they are under database/files/000/* thanks, Erick

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arabidopsis genome
by Vesselin Baev 11 Dec '09

11 Dec '09

Dear all, I was wandering if you plan to incorporate "get data" from arabidopsis TAIR DB? Thanks! -- ------------------------------------------------ Dr. Vesselin Baev Research Assistant Professor University of Plovdiv Dept. Molecular Biology Bioinformatics Group Tzar Assen 24 Plovdiv 4000, BULGARIA +359 32 261 (560) +359 89 43 80 945 Skype: vebaev vebaev(a)gmail.com baev(a)uni-plovdiv.bg CV: http://plantgene.eu/vebaev

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Command line execution
by Jordan Mendler 10 Dec '09

10 Dec '09

Hi all, I was wondering, is there a way to use Galaxy from the Command Line, or is it all web/point-and-click based? I would like to be able to write scripts to run workflows on new experiments that come off the sequencer, from the command line on Cron, so wondering if anything like this is possible with Galaxy. Thanks, Jordan

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FW: ChIP-Seq and Gene Ontology with Galaxy-UCSC
by Mary Mangan 09 Dec '09

09 Dec '09

I actually did an exercise that described how to get GO IDs and GO terms from UCSC Table Browser at the request of the ENCODE project folks who are doing similar stuff. In the UCSC Table Browser tutorial materials ( http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28 ) click the Exercises button. See Exercise 3 to walk through it. Mary Mary Mangan, PhD President OpenHelix LLC 65 Main St. Somerville MA 02145 phone: 888-861-5051 x9 email: mmangan(a)openhelix.com http://blog.openhelix.com From: galaxy-user-bounces(a)lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of Oscar V Camacho Sent: Tuesday, December 08, 2009 5:44 PM To: galaxy-user(a)bx.psu.edu Subject: [galaxy-user] ChIP-Seq and Gene Ontology with Galaxy-UCSC Hi, I am currently doing some ChIP-Seq experiments, to analyze the data I get from the PeakFinder of my choice I'm using the Galaxy tool from the UCSC browser to manipulate my intervals. What I have is a file in .BED format with the chromosome number, Start, End of the position and then I fetch the closest features and up to this moment everything is perfect but now that I have the positions of the nearest features to my putative binding sites I would like to get the gene symbol, description y GO for each one of them in a sort of table so as I can analyze it later on and make relationships. Is there a direct tool between Galaxy and a Gene ontology database? Any help about this topic will be appreciated. Thank you in advance.

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ChIP-Seq and Gene Ontology with Galaxy-UCSC
by Oscar V Camacho 09 Dec '09

09 Dec '09

Hi, I am currently doing some ChIP-Seq experiments, to analyze the data I get from the PeakFinder of my choice I'm using the Galaxy tool from the UCSC browser to manipulate my intervals. What I have is a file in .BED format with the chromosome number, Start, End of the position and then I fetch the closest features and up to this moment everything is perfect but now that I have the positions of the nearest features to my putative binding sites I would like to get the gene symbol, description y GO for each one of them in a sort of table so as I can analyze it later on and make relationships. Is there a direct tool between Galaxy and a Gene ontology database? Any help about this topic will be appreciated. Thank you in advance.

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Re: [galaxy-user] Question from yesterday
by Daniel Blankenberg 08 Dec '09

08 Dec '09

Hi David, Due to variations between genomes, there are often more than one MAF block per region. You can however, have 1 stitched FASTA block per region: Start with your BED file. Go to Fetch Alignments, select Stitch MAF Blocks Tool. Set Choose Intervals to your BED file. Select your Desired MAF source from the locally cached alignments or alignments in your History. Select desired Species. Click Execute. This new file will now have 1 FASTA alignment block per region with the total number of sequences equaling (# of regions) x (# of species). Dan Managadze, David (NIH/NLM/NCBI) [F] wrote: > Dear Dan, > > I just wanted to follow up: have you received my emails yesterday with questions? > > If not, then you can have a look at my questions here: > > Question 1: > I am trying to get the alignments of hg, panTro2, rheMac2. > -Input data: I have initial 877 already merged (unique) regions (hg18); > -I do multiple alignment and get 38,403 blocks; > Now I need to get the alignments one per region (which should be close to that 877 value, right?). > -I did "filter MAF blocks by species" and got 38,269 blocks; > -I did "Join MAF blocks by Species" and got 5,098 blocks! pretty far from 877! > > Could you please help me to solve this issue? What should I do to decrease the number of blocks to 877? > The data can be found in my history item called "MAF, IR, NEW". > > > Question 2: > I want to calculate pairwise distances between these alignments. Is it possible in Galaxy? I can not find it. > > Sorry that I am boring you with my questions but can not find other way (or person to ask about). > > David Managadze, PhD > > Postdoctoral Fellow > NCBI/NIH > Bethesda, MD > USA > > On Dec 7, 2009, at 4:15 PM, Daniel Blankenberg wrote: > > >> I noticed you are not looking at alignments between human and mouse, >> however the multiple blocks per region logic still holds true. >> >> Thanks, >> >> Dan >> >> Daniel Blankenberg wrote: >> >>> Hi David, >>> >>> Due to rearrangements etc. between the human and mouse genomes, there >>> are often multiple MAF blocks which overlap a single region. >>> >>> You can use the stitch MAF blocks tool, however, to create one FASTA >>> alignment block per region. This will create 876 FASTA alignment >>> blocks, each with 2 sequences. >>> >>> As far as 'I try "Stitch MAF blocks given a set of genomic intervals" >>> and I get 6,632! twice more than join! ', my guess is that you used >>> the MAF file in your previous step as the input intervals (using >>> implicit datatype conversion), resulting in twice as many 'sequences' >>> (2 per alignment block) as input intervals (MAF blocks). Be sure that >>> you are using your original bed file as the interval input. >>> >>> Let us know if this isn't the issue you are experiencing, >>> >>> >>> Dan >>> >>> >>> >>>> -------- Original Message -------- >>>> Subject: Re: [galaxy-bugs] Galaxy tool error report from >>>> david.managadze(a)nih.gov >>>> Date: Mon, 7 Dec 2009 14:44:02 -0500 >>>> From: Managadze, David (NIH/NLM/NCBI) [F] <managdav(a)ncbi.nlm.nih.gov> >>>> To: Nate Coraor <nate(a)bx.psu.edu> >>>> References: <20091207190211.9D3171989F(a)coltrane.bx.psu.edu> >>>> <4B1D525F.4010804(a)bx.psu.edu> >>>> <13191C8B-2095-4F72-A23C-C6C97369FF1B(a)nih.gov> >>>> <4B1D5572.7060909(a)bx.psu.edu> >>>> >>>> Thanks Nate, >>>> >>>> Sorry, can I ask you another question (can not find in forums) ? >>>> >>>> I am trying to get the pairwise alignments corresponding to my BED >>>> table. >>>> -Input data: I have initial 876 already merged (unique) regions (hg18), >>>> -I get 3,316 corresponding pairwise alignments (hg18, rheMac2) >>>> >>>> Now I need to get the alignments one per region (which should be >>>> close to that 876 value, right?) >>>> >>>> - I try "Join MAF blocks by Species" and get 3,316 blocks >>>> - I try "Stitch MAF blocks given a set of genomic intervals" and I >>>> get 6,632! twice more than join! >>>> >>>> Am I doing something wrong? I can not find the mistake. >>>> Which tool to choose? Join or Stich? My guess is join because I >>>> already have an alignment but why does not it decrease the amount of >>>> alignments at all and why idoes it remain almost 4x more than initial >>>> regions? >>>> >>>> Please help me to solve this problem (If you have an access to my >>>> history, it's in the one called "PAF"). >>>> Thanks, >>>> >>>> David Managadze, PhD >>>> >>>> Postdoctoral Fellow >>>> NCBI/NIH >>>> Bethesda, MD >>>> USA >>>> >>>> On Dec 7, 2009, at 2:20 PM, Nate Coraor wrote: >>>> >>>> >>>>> Hi David, >>>>> >>>>> Unfortunately there's no way to do this now, although there's a good >>>>> reason: you can go back and undelete history items, so numbering >>>>> would become very confused if you later undeleted an item. >>>>> >>>>> --nate >>>>> >>>>> Managadze, David (NIH/NLM/NCBI) [F] wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I have tried, it worked now :) >>>>>> >>>>>> Can I ask you a quick question? >>>>>> >>>>>> I am new in Galaxy. Sometimes I delete some of the steps in history >>>>>> and do something different, but the history number (I guess to >>>>>> remain unique) starts from the next one, not the one I deleted. >>>>>> So, I can have history items numbered like: 1,3,6,9,11 etc. instead >>>>>> of having 1,2,3,4,5. >>>>>> >>>>>> Is it possible to "reset" the numbering of the history items so >>>>>> that it does not count deleted items? >>>>>> Not a big problem but still it would be nice to have such a >>>>>> possibility. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> David Managadze, PhD >>>>>> >>>>>> Postdoctoral Fellow >>>>>> NCBI/NIH >>>>>> Bethesda, MD >>>>>> USA >>>>>> >>>>>> On Dec 7, 2009, at 2:07 PM, Nate Coraor wrote: >>>>>> >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> A momentary cluster problem caused this error. Please try >>>>>>> submitting the job again. >>>>>>> >>>>>>> --nate >>>>>>> >>>>>>> galaxy-bugs(a)bx.psu.edu wrote: >>>>>>> >>>>>>>> GALAXY TOOL ERROR REPORT >>>>>>>> ------------------------ >>>>>>>> >>>>>>>> This error report was sent from the Galaxy instance hosted on the >>>>>>>> server >>>>>>>> "main.g2.bx.psu.edu" >>>>>>>> ----------------------------------------------------------------------------- >>>>>>>> >>>>>>>> This is in reference to dataset id 950377 from history id 307838 >>>>>>>> ----------------------------------------------------------------------------- >>>>>>>> >>>>>>>> You should be able to view the history containing the related >>>>>>>> history item >>>>>>>> >>>>>>>> 8: Extract Pairwise MAF blocks on data 7 >>>>>>>> by logging in as a Galaxy admin user to the Galaxy instance >>>>>>>> referenced above >>>>>>>> and pointing your browser to the following link. >>>>>>>> >>>>>>>> main.g2.bx.psu.edu/history/view?id=37b126e5445be2d0 >>>>>>>> ----------------------------------------------------------------------------- >>>>>>>> >>>>>>>> The user 'david.managadze(a)nih.gov' provided the following >>>>>>>> information: >>>>>>>> >>>>>>>> >>>>>>>> ----------------------------------------------------------------------------- >>>>>>>> >>>>>>>> job id: 731079 >>>>>>>> tool id: Interval2Maf_pairwise1 >>>>>>>> ----------------------------------------------------------------------------- >>>>>>>> >>>>>>>> job command line: >>>>>>>> python /galaxy/home/g2main/galaxy_main/tools/maf/interval2maf.py >>>>>>>> --dbkey=hg18 --chromCol=1 --startCol=2 --endCol=3 --strandCol=6 >>>>>>>> --mafType=PAIRWISE_hg18_rheMac2 >>>>>>>> --interval_file=/galaxy/home/g2main/galaxy_main/database/files/000/950/dataset_950316.dat >>>>>>>> --output_file=/galaxy/home/g2main/galaxy_main/database/tmp/job_working_directory/731079/galaxy_dataset_950377.dat >>>>>>>> --indexLocation=/galaxy/home/g2main/galaxy_main/tool-data/maf_pairwise.loc >>>>>>>> >>>>>>>> ----------------------------------------------------------------------------- >>>>>>>> >>>>>>>> job stderr: >>>>>>>> None >>>>>>>> ----------------------------------------------------------------------------- >>>>>>>> >>>>>>>> job stdout: >>>>>>>> None >>>>>>>> ----------------------------------------------------------------------------- >>>>>>>> >>>>>>>> job info: >>>>>>>> Unable to queue job for execution. Resubmitting the job may >>>>>>>> succeed. >>>>>>>> ----------------------------------------------------------------------------- >>>>>>>> >>>>>>>> job traceback: >>>>>>>> None >>>>>>>> ----------------------------------------------------------------------------- >>>>>>>> >>>>>>>> (This is an automated message). >>>>>>>> _______________________________________________ >>>>>>>> galaxy-bugs mailing list >>>>>>>> galaxy-bugs(a)lists.bx.psu.edu >>>>>>>> http://lists.bx.psu.edu/listinfo/galaxy-bugs >>>>>>>> >>>> _______________________________________________ >>>> galaxy-lab mailing list >>>> galaxy-lab(a)lists.bx.psu.edu >>>> http://lists.bx.psu.edu/listinfo/galaxy-lab >>>> >>> _______________________________________________ >>> galaxy-bugs mailing list >>> galaxy-bugs(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-bugs >>> > >

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fetch sequences
by Courtney Babbitt 07 Dec '09

07 Dec '09

Hello, I'm trying to fetch sequences from Hg18 using a 3 column tab- delimited file (chr coord1 coord2), but the pulldown tab "Fetch sequences corresponding to Query" isn't letting me select any file. How do I get this tool to work? Thanks, Courtney

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galaxy behind proxy
by Gunnar Raetsch 01 Dec '09

01 Dec '09

Hi everybody, I have a problem with some proxy settings for our galaxy instance. Our admins want to have the server protected better and put it behind a firewall/proxy. That all seems to work after switching on the firewall, but not the external data sources (like biomart or UCSC browser). I did not find an configuration option for galaxy, so I just use the environment variable http_proxy. If I try biomart without setting http_proxy, then I get this error message: The remote data source application may be off line, please try again later. Error: [Errno socket error] (111, 'Connection refused') if I set http_proxy to dmzproxy.tuebingen.mpg.de:8080, then I get this error: The remote data source application may be off line, please try again later. Error: [Errno url error] invalid proxy for http: 'dmzproxy.tuebingen.mpg.de:8080' These errors appear after finishing with biomart and it tries to send the data back to the galaxy instance. What is the right way to get these tools to work behind a firewall/ proxy? Thanks a lot for your help in advance, Gunnar +-------------------------------------------------------------------+ Gunnar Rätsch http://www.fml.mpg.de/raetsch Friedrich Miescher Laboratory Gunnar.Raetsch(a)tuebingen.mpg.de Max Planck Society Tel: (+49) 7071 601 820 Spemannstraße 39, 72076 Tübingen, Germany Fax: (+49) 7071 601 801

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