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

RNASeq analysis questions
by Aarti Desai 11 Feb '11

11 Feb '11

Hi, I am using galaxy to analyze some RNASeq data. I have a couple of questions with regards to it: 1. When we are uploading data, one of the fields to be populated is "Genome". Why or where is galaxy using the genome information during file upload? 2. During Cuffcompare analysis, we can provide 3 files, two GTF files output from cufflinks and a reference annotation file. When cuffcompare how does it use the annotation file? 3. If cuffcompare is run using one cufflink GTF file and one reference annotation file, what are we supposed to do during cuffdiff analysis where you have to provide 2 sam/bam files? Is there any documentation/manual (except for what is on the UI) around that can help answers these (and some other basic questions I have). Thanks a lot for your help. Regards, Aarti

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entrez ID to Refseq or gene symbol
by giovanni stefani 10 Feb '11

10 Feb '11

Hello, does anyone know how to convert entrez I.D. to either Refseq ID or Gene Symbols? I have found resources on Refseq to Gene Symbol conversion, but I can't find anything on Entrez I.D. The genome I work with is C. elegans. Any suggestion will be greatly appreciated. Best, Giovanni

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Extract sequences from [gtf file] + [genome FASTA file]
by Karen Tang 10 Feb '11

10 Feb '11

Hi Galaxy people, I have transcripts predicted by Cufflinks that are in a gtf file. How can I extract the sequences corresponding to those transcripts, using Galaxy? [Cufflinks transcript predictions in gtf file] + [Genome sequence in FASTA file] ---> [FASTA file of transcript sequences] My genome is a custom genome (not at UCSC). --------- I'll also need to do the same thing, except my predicted transcripts are in a Scripture bed file. Thanks for your help! Karen Tang :) Plant Biology University of Minnesota

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Re: [galaxy-user] Inquiring
by Yan Luo 10 Feb '11

10 Feb '11

Dear Nate, Thanks for your quick response. I appreciate, it is very important for us to use it. We have problem recently. (1) In fact, I can't find the file "paster.log". The problem is that recently we expanded our gluster(Linux sever) and did the rebalance that has some bugs. Some of files permission have been changed. So we can't use User/register righr now, when we tried, we got the sever error, do you have any idea how to fix it? (we can change the ownships/read and write permission for some files manually, but we don't know which files and where they are?) (2) We want to reboot the Galaxy, should we first stop and start as follows? $ sh run.sh --stop $ sh run.sh Is there any difference if I use "-daemon" flag? Last times, my colleague started using "./run.sh". How to stop it? If "$ sh run.sh --stop" doesn't work (I didn't try yet, ), how can I find the process (Linux) that is running by Galaxy and kill it? (3) Could you please let me know if there is a default administrator user/password for galaxy. I want to add an administrator user, how can I do that? According to the instruction, I will change a line of "universe_wsgi.ini" as follows. How can I set/get my password? admin_users = yan.luo(a)email.com (4) I found our "universe_wsgi.ini" contains the following setting, should I remove "#" before this line, stop and start galaxy? #allow_user_creation = True I plan to restart our galaxy, if it is possible, could you please let me know your phone #? I can call you sometime today, or if you prefer, I can give you my phone #. Looking forward to hearing from you. Best Wishes, Yan Luo, Ph.D. NIH On Thu, Feb 10, 2011 at 10:01 AM, Nate Coraor <nate(a)bx.psu.edu> wrote: > Hi Yan, > > I've moved this discussion to the galaxy-dev list since it pertains to a > local installation of Galaxy. > > Responses to your questions follow, in-line. > > Yan Luo wrote: > > Dear Sir, > > > > (1)We installed Galaxy, but recently the user can't registered and got > the > > following error, how can we fix it? > > > > Sever error > > An error occurred. See the error logs for more information.(To turn debug > on > > to display ...). > > Since debug = False in universe_wsgi.ini, you should be able to find a > more detailed error message in the log file. If starting Galaxy with: > > % sh run.sh --daemon > > The default log file is 'paster.log' in Galaxy's root directory. > > > (2) Could you please let me know if there is any command to stop galaxy? > > If starting with the --daemon flag (as above), you can use: > > % sh run.sh --stop-daemon > > If running in the foreground, you can use Ctrl-C to terminate the > process. There is a recent bug whereby Ctrl-C is ineffective on some > platforms under Python 2.6 - in this case you will have to kill/pkill > the process manually. We are working on a fix for the latter. > > > (3) If I reset universe_wsgi.ini file and want to set an administrator > > user(I can add a line in the above file), how can I get the password? > Should > > I stop galaxy(See question 2) first? then run "./setup.sh" and > "./run.sh". > > setup.sh would have only been necessary prior to running Galaxy the > first time, however, this step has recently been removed. If you are > referencing documentation that still refers to setup.sh, please let us > know so we can update it - I did notice this was still on the > "Production Server" page, so I removed it from there. > > You no longer need to run setup.sh at all. > > > (4) If I run "setup.sh", will a new file "universe_wsgi.ini" be > generated? > > if I want to change this file,should I edit it before "run.sh" and after > > "setup.sh". Is it right? > > setup.sh and its replacements in run.sh and the Galaxy application > itself never overwrite files, they only create files from sample files > if they do not exist. > > > (5) I read some of your docs, command "sh setup.sh"(sh run.sh) and > > "./setup.sh"(./run.sh), which one is correct under Linux? > > Both syntaxes are effectively the same in most cases. > > --nate > > > > > Looking forward to hearing from you. > > > > Best Wises, > > > > Yan Luo, Ph.D. > > NIH > > < > http://int.ask.com/web?siteid=10000861&webqsrc=999&l=dis&q=By%20the%20way, > > > > > _______________________________________________ > > galaxy-user mailing list > > galaxy-user(a)lists.bx.psu.edu > > http://lists.bx.psu.edu/listinfo/galaxy-user > >

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trouble shooting on standalone version of fastx_clipper
by Philippe MONCUQUET 10 Feb '11

10 Feb '11

Hi, Thank you for the very nice tool you are developping. I'm currently having some problems to run the standalone version of fastx_clipper on my own computer. Here is the bug report : fastx_clipper: failed to open input file 'path': Value too large for defined data type It seems like it's an error linker to gzip and files > 4Go but i don't see the point. Do you have a clue of what i could try to solve that. thank you Philippe Moncuquet IR Bioinformatician Olivier Pourquié's team IGBMC 1 rue Laurent Fries BP 10142 67404 Illkirch CEDEX / France Tél +33 (0) 3 88 65 33 98 pmcqt(a)igbmc.fr

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Inquiring
by Yan Luo 10 Feb '11

10 Feb '11

Dear Sir, (1)We installed Galaxy, but recently the user can't registered and got the following error, how can we fix it? Sever error An error occurred. See the error logs for more information.(To turn debug on to display ...). (2) Could you please let me know if there is any command to stop galaxy? (3) If I reset universe_wsgi.ini file and want to set an administrator user(I can add a line in the above file), how can I get the password? Should I stop galaxy(See question 2) first? then run "./setup.sh" and "./run.sh". (4) If I run "setup.sh", will a new file "universe_wsgi.ini" be generated? if I want to change this file,should I edit it before "run.sh" and after "setup.sh". Is it right? (5) I read some of your docs, command "sh setup.sh"(sh run.sh) and "./setup.sh"(./run.sh), which one is correct under Linux? Looking forward to hearing from you. Best Wises, Yan Luo, Ph.D. NIH <http://int.ask.com/web?siteid=10000861&webqsrc=999&l=dis&q=By%20the%20way,>

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ISMB/ECCB Workshop Proposal, due Friday, Feb 11
by Dave Clements 09 Feb '11

09 Feb '11

Hello all, The Galaxy Project is putting together a workshop proposal for ISMB/ECCB. The theme of the proposed workshop will be "Genomics for Emerging Models" or "Genomics: Flying without a reference". We want to have 4 talks that show attendees particular solutions to challenges that arise when working with organisms that don't have a closely related reference genome available. *The proposal is due Friday, February 11*, in just two days. Our aim is to highlight the solutions, with Galaxy gluing it all together, but not being the focus of the workshop. We want to highlight the science while also demonstrating the power of Galaxy. If you have an approach that addresses a challenge with non-model organisms (and that approach involves Galaxy!), please consider presenting it at ISMB as part of this workshop proposal. *If we get more than 4 proposals, we'll make a final call on what to include in the proposal on Thursday night. * Workshop guidelines and info are at http://www.iscb.org/ismbeccb2011-submission-details/workshops. Please let me know if you have any questions. Thanks, Dave C -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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uploading fastq
by Keith E. Giles 09 Feb '11

09 Feb '11

My fastq files won't queue up into galaxy. Any ideas why?

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operating on, and getting at, large files in galaxy...
by Nick Schurch 09 Feb '11

09 Feb '11

Hi all, I've recently encountered a few problems when trying to use Galaxy which are really driving me away from using it as a bioinformatics platform for NGS. I was wonderinf if there are any simple solutions that I've missed... Firstly, It seems that while there are a few solutions for getting large files (a few GB) into a local install of galaxy without going through HTTP, many tools that operate on these files produces multiple, uncompressed large files which quickly eat up the disk allocation. This is particularly significant in a workflow that has multiple processing steps which each leave behind a large file. With no way to compress or archive files produced by intermediate steps in a workflow, and no desire to delete them since I may need to go back to them and they can take hours to re-run, the only two remaining options seem to be to save them and then delete them. And this brings me to the second problem. Getting large files out of Galaxy. The only way to save large files from Galaxy (that I can see) is the save icon, which downloads the file via http. This take *ages* for a large file and also causes big headaches for my firefox browser. I've taken a quick peek at the Galaxy file system to see if I could just copy a file, but its almost completely indecipherable if you want to find out what file in the file system corresponds to a file saved from a tool. Is there some way to get the location of a particular file on the galaxy file system, that I can just copy? -- Cheers, Nick Schurch Data Analysis Group (The Barton Group), School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK Tel: +44 1382 388707 Fax: +44 1382 345 893 -- Cheers, Nick Schurch Data Analysis Group (The Barton Group), School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK Tel: +44 1382 388707 Fax: +44 1382 345 893

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(no subject)
by Ying Zhang 09 Feb '11

09 Feb '11

Hi: My name is Ying, a postdotoral associate working in Yale university. I am trying to use tophat in galaxy to analyze paired-end RNA-seq data, however, after I groomer and use tophat to analyze them, I only got an empty file. I am wondering what is the problem here. One thing I am concerned is that my files is kind of large, e.g., for each end I got a file with 20.7 gb, so totally 41.4 gb for both ends of this sample. So do you think it is because the files are too big? Also when the genome center sent me the data, they already separate the two ends into two files, so I uploaded two files for one sample, but when do tophat analysis, do I need to merge those two files into one file? do you know what is the usual parameter set up for paried-end RNA-seq analysis(with a 300 bp fragment)? Thank you very much! I really appreciate your help! Best Ying Zhang, M.D., Ph.D. Postdoctoral Associate Department of Genetics, Yale University School of Medicine 300 Cedar Street,S320 New Haven, CT 06519 Tel: (203)737-2616 Fax: (203)737-2286

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