December 2011 - galaxy-user - lists.galaxyproject.org

SNPEff - Reports Gain of Stop Codon as FRAME_SHIFT in some cases
by John David Osborne 18 Jan '12

18 Jan '12

Hi Pablo, Correct me if I am wrong, but I believe that SNPEff doesn't check the inserted sequence when computing the effect of an insertion? For instance an insertion of TTTA will be reported as a frameshift mutation. In the majority of cases this is fine, however if the current reading frame from the ORF annotation is the negative strand and the correct frame is selected the new codon will be: TAA T… The TAA is actually a stop codon, so the real effect of this insert should be insertion of a STOP CODON, not a frame shift in this instance. This is minor I know, but I though to report and make people aware. I am using version 2.02 of SNPEff, but I don't see this fix reported up to 2.04. -John

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Trouble getting tophat to run on built-in index genome
by Noa Sher 18 Jan '12

18 Jan '12

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Fixed parts inside workflows
by Saadeh, Heba 18 Jan '12

18 Jan '12

Dear All, I used to work with galaxy web site gladly, until I need to apply one workflow with (tens of join operations) on tens of datasets. so the problem is that if I need to run the workflow, each time I need to indicate the input datasets for each join operation and that is not interesting at all, and very time consuming. "although they are the same for each input file, in theory what I need to change is only the main input file, and leave the other files of the join operations the same, sound easy :)". I have read the comments for the "Workflows & Multiple datasets" post, on "how to run a workflow for multiple input files", and its now only working on galaxy-central, which I downloaded and used and it works fine and will solve one side of my problem the remaining will be with the fixed part inside the workflow. One last comment: the folder uploading functionality in galaxy-central is not working properly with me, the process continue until running the "uploading commands" but the files are all with 0 size, the same process on galaxy-dist works well... Much appreciated, heba --- Heba Saadeh Ph.D. Student Dept. of Medical and Molecular Genetics, Medicine School, King's College London, Guy's Hospital, 8th floor Tower Wing, London, SE1 9RT. Office: +44(0)20 7188 3715 ________________________________________ From: galaxy-user-bounces(a)lists.bx.psu.edu [galaxy-user-bounces(a)lists.bx.psu.edu] On Behalf Of Adhemar [azneto(a)gmail.com] Sent: 19 December 2011 18:35 To: Dannon Baker Cc: galaxy-user(a)lists.bx.psu.edu Subject: Re: [galaxy-user] Workflows & Multiple datasets I already tested and it's working like a charm. Thank you very much Dannon. -Adhemar 2011/12/19 Dannon Baker <dannonbaker(a)me.com<mailto:dannonbaker@me.com>> Ahh, I should have specified, that changeset is in the galaxy-central repository and has not been moved to galaxy-dist yet. I think we're testing a few more things, but this should happen in the near future, at which point you could simply update from galaxy-dist as usual, or you could pull directly from galaxy-central right now if you'd like. -Dannon On Dec 19, 2011, at 12:50 PM, Adhemar wrote: > Dannon, > Thanks for the immediate reply. > I just retrieved the latest code from the repository and it's not working > > $ hg summary > parent: 6298:b258de1e6cea tip > > > I also tried 'hg pull -u -r 6368:de03f821784b' but it says: > > pulling from https://bitbucket.org/galaxy/galaxy-dist > abort: unknown revision '6368:de03f821784b'! > > > How or when can I update to the release you mentioned? > Thanks, > -Adhemar > > > 2011/12/19 Dannon Baker <dannonbaker(a)me.com<mailto:dannonbaker@me.com>> > Adhemar, > > This was a bug that has been fixed as of changeset 6368:de03f821784b, which should be available on main.g2.bx.psu.edu<http://main.g2.bx.psu.edu> in the near future. If you're running a local instance, you'll find this resolved as soon as you update to that changeset or higher. > > Unfortunately, there isn't a fast way to copy datasets into a data library from multiple histories at once. I think you might find it faster to use the standard "Copy Datasets" functionality in the history Options menu to move everything you'd like into a single new history, and from there move it into a library. This Copy Datasets action allows you to select an individual history to copy from, instead of manually changing to the history first, so it should save you some time to do it that way. > > -Dannon > > > On Dec 19, 2011, at 12:12 PM, Adhemar wrote: > > > Hi, > > I was searching for how to run a workflow for multiple input files and I was very happy to find it's already implemented as mentioned here: http://wiki.g2.bx.psu.edu/News%20Briefs/2011_05_20 > > > > The problem is that it's not working for me. When I select two files, for example, it runs the workflow only in the first file. Even if I check 'Send results to a new history', it only creates a new history called 'test 1' and not the others. Is my instance somehow misconfigured or it's happening to others as well? > > > > I'm also looking for a way to add datasets to a library from different histories. Do I really need to open each history one by one and use 'Import datasets from your current library'? > > > > Thank you, > > Adhemar > > > > > > > > ___________________________________________________________ > > The Galaxy User list should be used for the discussion of > > Galaxy analysis and other features on the public server > > at usegalaxy.org<http://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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Merge FASTQ Databases
by Edward Turk 11 Jan '12

11 Jan '12

Hi Galaxy Users, Can FASTQ Databases be merged using Galaxy? Thanks, Edward

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Error Handling in Galaxy Workflows ?
by John Major 06 Jan '12

06 Jan '12

Hi All- Is there any plumbing in place for handling errors that occur in component tools of workflows? I'm thinking about a case where you might want to follow path 'A' if a tool succeeds, but path 'B' if there is some specific kind of exception, and fail completely if any other error is thrown. If this is in place, a pointer to the relevant docs would be awesome. I've looked around and did not come up with anything. Thanks! John

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ftp upload
by Gabor Bartha 03 Jan '12

03 Jan '12

I have tried to use ftp to upload files to main.g2.bx.psu.edu but the jobs have been failing with: 421 service not available, remote server has closed connection after about 1.5GB. Isn't ftp the way you are supposed to upload large files? The file I am uploading is ~6GB in size. Gábor Bartha, Ph.D. Director of Information Sciences Synergenics, LLC 863 Mitten Rd., Suite 101 Burlingame, CA 94010 650-777-5202

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problem upload data file
by Eric Guo 03 Jan '12

03 Jan '12

Hi everyone, I'd like to upload my sequencing data file, 36 GB, onto galaxy. My data is on a computer cluster in my institute. So I use ssh shell ftp commands to connect to galaxy and upload the data(ftp> put filename). And the connection appears to be fine as far as I can tell. I tried few times. Every time the uploading is fine in the beginning. However, when about 12 GB of my dataset is uploaded (according to Galaxy upload file page), the upload stops, and an error message pop up in the terminal on my Mac saying "a broken pipeline". I never had this problem before when I was using FTP programs like CyberDuck. Has anyone have similar problems using ssh command lines to upload data? What's the correct way to upload data from a computer cluster? Thanks in advance for your help. -Eric

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Not able to get data from UCSC table browser
by Peng Yu 03 Jan '12

03 Jan '12

Hi, I'm trying to get data from UCSC table browser. However, the browser always show "Waiting for main.g2.bx.psu.edu...". Is there any problem with the galaxy server? -- Regards, Peng

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Bam Format
by Giuseppe Petrosino 29 Dec '11

29 Dec '11

Dear all, I downloaded a file in .BAM format and want to transform it into .BED format. What can I do on Galaxy? Thanks a lot! Giuseppe

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(OperationalError) unable to open database file
by Cai Shaojiang 28 Dec '11

28 Dec '11

Dear friends, We are trying to install galaxy on the server (ubuntu 11), just by following the steps on the page "Get Galaxy: Galaxy Download and Installation" of galaxy wiki. But when we start running it, it shows the following error message. OperationalError: (OperationalError) unable to open database file u'INSERT INTO galaxy_session (create_time, update_time, user_id, remote_host, remote_addr, referer, current_history_id, session_key, is_valid, prev_session_id, disk_usage) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)' ['2011-12-29 04:52:46.575702', '2011-12-29 04:52:46.575719', None, '10.50.70.45', '10.50.70.45', None, None, '5a38b2a7e6d77a7145726cb0881eadf6', 1, None, None] It seems something wrong with the write permission. Could you give any hint where the problem could be? Thanks. Best regards. Yours: Cai

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