galaxy-user March 2011

galaxy-user@lists.galaxyproject.org

75 participants
96 discussions

Problem Adding a Custom Build in Trackster
by Liisa Koski 08 Mar '11

08 Mar '11

Hello, I am trying to 'Add a Custom Build' to my local instance of Galaxy/Trackster. There seems to be a problem when I enter the chromosome length info, both when I paste directly on the screen and when I use the upload button (for the .len file). After I press Submit I can see the Name and Key info that I specified but it always says that the 'Number of Chroms' is 0. Is there a bug or I am doing something wrong? Thanks for you help, Liisa

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Referencing data library directly from tool's input parameter dropdown.
by Rodriguez, Aaron (NIH/NCI) [C] 07 Mar '11

07 Mar '11

Hello all. First of all thanks to Galaxy developers and supporters for this great tool -- I'm experimenting with adding my custom tools to galaxy and I'm very impressed with how simple galaxy makes this process. Some of the tools that I'm adding to my local instance take reference files as a parameter. These files are often large and fairly static. I understand that I can create a data library where users can select the reference file needed and import into "history" for analysis. However, I would like to know if it's possible for a tool's input parameter (dropdown) to enumerate these files from a public data-library (to avoid the steps needed to import from library into history) and have that file pathname become the value for my parameter? As an alternative, would it be possible to load such a drop down from files (of a certain type) existing at some predefined system path? Thanks in advance, -AR

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Re: [galaxy-user] [galaxy-bugs] For small RNA analysis
by Jennifer Jackson 07 Mar '11

07 Mar '11

Hello, Yes, and this tutorial can help to get you oriented: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise Please let us know if we can help more (using galaxy-user(a)bx.psu.edu please for data/tool questions), Best, Jen Galaxy team On 2/16/11 9:10 AM, Jianquan Wang wrote: > Dear Sir/Madam, > > I have one set of small RNA sequence data. I am wondering whether I can use > Galaxy to analyze it. > Thank you. > > Jianquan Wang > > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

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Bowtie Job doesn't start
by Felix Hammer 07 Mar '11

07 Mar '11

Hi, just trying to use Bowtie, but the job does not start. Is there somthing wrong with the server at the moment? Felix

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Re: [galaxy-user] Fwd: Need a generous help regarding uploading
by Jennifer Jackson 07 Mar '11

07 Mar '11

Hi Vasu, Very sorry to hear that you are still having problems. Have you been able to do the update? It was not clear from your email. The latest is: http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r ca0c4ad2bb39 When you reply, could you note which revision you are using (perhaps you are pulling from galaxy-central instead?) Thanks for helping us to diagnose the problem, Jen Galaxy team On 1/3/11 12:05 PM, vasu punj wrote: > NO I am still unable to get it through. Any help in this regard will be > apprceiated. > Vasu > > --- On *Mon, 1/3/11, Jennifer Jackson /<jen(a)bx.psu.edu>/* wrote: > > > From: Jennifer Jackson <jen(a)bx.psu.edu> > Subject: Re: [galaxy-user] Fwd: Need a generous help regarding uploading > To: "vasu punj" <punjv(a)yahoo.com> > Cc: "galaxy-user(a)bx.psu.edu" <galaxy-user(a)bx.psu.edu> > Date: Monday, January 3, 2011, 1:59 PM > > Hello Vasu, > > Are you still having problems? Or did this other reply help? > http://gmod.827538.n3.nabble.com/Bam-file-after-Tophat-run-td2089789.html#a… > > If the problem is persistent, Galaxy needs to be updated to get better > UI support for downloading BAM files. > > Hopefully the problem can be resolved, but please let us know if you > need more help. > > Thanks! > > Jen > Galaxy team > > > On 12/15/10 12:23 PM, vasu punj wrote: > > I have submited your email to share job 31 and 25 are the Tophat runs > > which I am trying to save as bam files from Floppy icon. > > The job is run on our University cluster. I have alos enclosed screen > > shot for your ready reference. > > vasu > > > > --- On *Wed, 12/15/10, Jennifer Jackson /<jen(a)bx.psu.edu > > Hello Asifullah, > > > > It would be helpful if you would be able to share your history. > Please > > note which exact datasets (by number) you are having problems saving. > > > > Use Options -> Share or Publish -> click on the button to Share via > > link > > and then email that to me. > > > > Thank you, > > > > Jen > > Galaxy team > > > > On 12/15/10 7:56 AM, vasu punj wrote: > > > I have done the same it gav eme bam index file when i removed the > > > extension index or as such it come out to be not right bam file > > format > > > as recognized by various tools > > > Thanks > > > Date: Wednesday, December 15, 2010, 9:52 AM > > > > > > Hello Asifullah, > > > > > > Click on the "save" icon for the dataset to initiate a > download. This > > > icon is shaped like a little purple disk on the very left side > of the > > > dataset's box in the right history pane. > > > > > > Hopefully this is helpful, > > > > > > Thank you, > > > > > > Jen > > > Galaxy team > > > > > > On 12/15/10 7:47 AM, vasu punj wrote: > > > > Hi, > > > > Can we save Bam file from Tophat out put if so how can we do that > > > please. > > > > Thanks. > > > > Date: Wednesday, December 15, 2010, 9:38 AM > > > > > > > > Hello Asifullah, > > > > > > > > The Galaxy tool "Get Data -> Upload File" has instructions for > > > > uploading > > > > data to the FTP server. We recommend using the 3rd party utility > > > > FileZilla as a desktop FTP client. > > > > > > > > http://file-zilla.com/ > > > > > > > > Hopefully this will get you started, > > > > > > > > Best! > > > > > > > > Jen > > > > Galaxy team > > > > > > > > ps: In the future, if you could send questions directly to > > > > galaxy-user(a)bx.psu.edu > > > > >> *Subject: **Need a generous help regarding uploading* > > > > >> > > > > >> Dear All, > > > > >> > > > > >> I am in trouble to upload 1.2Gb illumine data on Galaxy > page for > > > > >> subsequent assembling and analysis steps. I am basically a > > > biologist > > > > >> and new regarding utility of modern bioinformatics tools. > > some one > > > > >> have suggested to upload first your data on a http web page > > > then it > > > > >> would be easy to be uploaded on GALaxy. But it is also not > > > possible > > > > >> for me as having little computer knowledge. So could some one > > > > help me > > > > >> generously regarding these issue. I will highly appreciate > > > > his/her help. > > > > >> > > > > >> Regards > > > > >> Asifullah Khan > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > galaxy-user mailing list > > > > > galaxy-user(a)lists.bx.psu.edu -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

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upload of Zea mays genome to galaxy?
by karlerhard＠berkeley.edu 06 Mar '11

06 Mar '11

Hello, I'm interested in using the galaxy tools to analyze some transcriptome libraries I made of maize seedlings. Would it be possible to upload the maize reference genome to the galaxy browser? It's available at the following website: http://ftp.maizesequence.org/current/ Hope this can be done, would be really exciting! Thanks, Karl

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Map with Bowtie job is waiting to run for more than 1 hour...
by Daniel Fernandez 05 Mar '11

05 Mar '11

Hi, I tried running map with bowtie but it says: job is waiting to run... any suggestions? Thanks!

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upload large data set
by Yanji Xu 05 Mar '11

05 Mar '11

Dear Sir/Madam, I installed galaxy in my local server, then I tried to upload a 4.7 Gb fastq file into galaxy, but failed. Below is the error message. OverflowError: signed integer is greater than maximum How could I upload large data files into galaxy and process the data? Any information from you would be quite appreciated. Thanks, Dicty

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Join and Sort in Galaxy
by Felix Hammer 04 Mar '11

04 Mar '11

Hello, I have some questions about the Join and Sort tools in Galaxy. How are they implemented? Just the standard unix sort and join? I have a quite large tab file (~1,5 million lines), I want to join with a somewhat smaller file (~20 000 lines). How long will this approximately take? Is there a way to view the progress? Can I gain performance if do a sort on the column I want to join? thx, Felix

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Requesting your help for a Survey on data privacy while using workflows
by vishal dwivedi 04 Mar '11

04 Mar '11

Dear Galaxy Users, We are researchers at Carnegie Mellon University who are conducting a survey of users who compose web services in their workflows to build applications. One of the goals of this survey is to better understand the privacy concerns of web service users (or lack thereof), and how well users are able to resolve these concerns. Even if you have no data privacy and security problems while using web services, we would still appreciate your feedback because that would give us a better perspective of the problem scenario. Please take time to fill the following questionnaire: https://www.surveymonkey.com/s/RCC7XWT<https://www.surveymonkey.com/s/Y9FM836> The survey consists of maximum 17 questions and can be completed in about 10 minutes. There are no correct or incorrect responses. This survey is approved by CMU Institutional Review Board (IRB), and would follow the appropriate safety protocols set by the IRB (Protocol Number: HS11-091). All responses would be treated confidentially and will not be traceable to individual respondents. Thank you in advance for your assistance and time !! Best Regards, Vishal Dwivedi and Kun Niu Carnegie Mellon University, Pittsburgh, USA. Email: vdwivedi(a)cs.cmu.edu & kunn(a)andrew.cmu.edu

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galaxy-user March 2011