January 2013 - galaxy-user - lists.galaxyproject.org

nebula suite / _chiphorde.log not found
by Sarah Maman 07 Jan '13

07 Jan '13

Hello, I 've integrated nebula suite in my local instance of galaxy but here is the error message received when running ChipMunk analysis : Galaxy cannot stat a file "_chiphorde.log" in the job working directory. Do you have any idea ? Thanks in advance, Sarah

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(no subject)
by Eric Guo 07 Jan '13

07 Jan '13

http://hard-mobile.com/fkjbgs.php?ffij=ffij

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Add new page server error
by Aaron Stonestrom 04 Jan '13

04 Jan '13

When logged into main trying to create a new shared page under "Add new page" in Saved Pages, entering any page title and selecting Submit gives me: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Thanks for any help,

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Error Running CuffCompare on Galaxy Server
by Samit Watve 04 Jan '13

04 Jan '13

Hi, I'm attempting RNA-seq data analysis on *Vibrio cholerae* samples, at galaxy main https://main.g2.bx.psu.edu/. I was able to align transcripts using Ion Torrent's TMAP aligner. I uploaded the BAM files and used the cufflinks tool, which gave me FPKM scores for various transcripts. Now I want to extract the relevant gene_id for each mapped transcript using a reference genome. I tried using CuffCompare for this purpose using a reference file from the UCSC archaea database or using a FASTA file from history. In either case, cuffcompare gives me an error. Error1: (When using a reference genome from the UCSC archaea database) An error occurred running this job:*cuffcompare v2.0.2 (3522) No sequence data found for dbkey vibrChol1, so sequence data cannot be used. cp: cannot stat `/galaxy/main_pool/pool4/tmp/job_working_directory/004/846/4846005/cc_output.input1.refmap': No such file or directory cp: cannot stat `* * * Error 2: (When using a reference genome from history) An error occurred running this job:*cuffcompare v2.0.2 (3522) cuffcompare -o cc_output -r /galaxy/main_pool/pool1/files/005/515/dataset_5515739.dat -s ref.fa ./input1 Error running cuffcompare. You are using Cufflinks v2.0.2, which is the most recent release. No fasta index found for ref* * * Could you help me figure out what's going on? Thanks, -Samit Regards, Samit Watve Graduate Teaching Assistant, School of Biology, Georgia Institute of Technology PhD Student at the Hammer Lab, Office: Cherry Emerson, 218-E, 310 Ferst Drive Atlanta GA School of Biology, Georgia Institute of Technology Lab Page: http://www.hammerlab.biology.gatech.edu/

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galaxy test dataset listing
by Sun, Wenping [USA] 04 Jan '13

04 Jan '13

Hello, It is good to see there are some testing dataset in fastq format from galaxy s3. Is there any brief information about the test data? For example, RNAseq or Chipseq, etc? Many thanks, Kathryn

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Re: [galaxy-user] Batch jobs...
by Neil.Burdett＠csiro.au 03 Jan '13

03 Jan '13

Do i need to modify a setting in universe_wsgi.ini or somewhere then ? As I attach screenshots of what I've got (I have a recent subversion checkout)... Thanks Neil [cid:image001.jpg@01CDB754.FC6C6330] [cid:image002.jpg@01CDB754.FC6C6330]

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Building a combined annotated transcriptome to use as a reference annotation in RNA-Seq analysis
by Davide Degli Esposti 03 Jan '13

03 Jan '13

Dear all, I am analyzing RNA-Seq data and I would like to compare my cufflinks transcripts to an annotated transcriptome. Following the steps described in the paper by Trapnell et al Nature Biotechnology, 2010, I have read that authors ran cuffcompare against a combined annotated transcriptomes of the UCSC known genes, Ensembl and Vega. My question is how do you build such a combined file? For the moment, I was able just to compare my data with an annotated transcriptome obtained only by UCSC. I thank you for your help Best regards Davide Degli Esposti --- Davide Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel. +33 4 72738036 Fax. +33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France ----------------------------------------------------------------------- This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use -----------------------------------------------------------------------

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galaxy cloudman login
by Sun, Wenping [USA] 02 Jan '13

02 Jan '13

Hello, I have galaxy cloudman running and had tried one time success to log in to retain the previous data and history after re-launching followed by 1st time restart. Today I am re-launching again along with the correct size of ebs volumes that I adjusted earlier. However, my login is not recognized at all ("error:no such user...."). I tried several time of terminating and restarting and it is still the same. My admin which is same as the login was able to retained every time. What's the issue with the log in?? It is taking time to repeat previous data/history. I need your help to retrieve my login. Thank you in advance, Kathryn

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January 2013 Galaxy Update
by Dave Clements 02 Jan '13

02 Jan '13

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Seqpos output not visible in Safari/Firefox/Chrome
by Biswajyoti Sahu 02 Jan '13

02 Jan '13

Hello, I am using the Cistrome/Galaxy for the ChIP-seq analysis. Recently i am encountering two problems, first is with the Genomic interval operation where i am not able to intersect or subtract the bed files. Second is with the Seqpos motif tool. The Seqpos analysis runs fine, however when i try to visualize the Cistrome motifs it gives me a blank page with the following message: "Please use a frames compatible browser when viewing this output". I guess all the new browsers are frame compatible and in recent past i was able to visualize all the motifs and Seqpos output. The same is also happening with a colleague's computer. Looking forward to your response on this and any possible solution to overcome. Br, Sahu. Biswajyoti Sahu, Ph.D. Institute of Biomedicine, Physiology POB-63, Haartmaninkatu-8 FI-00014, University of Helsinki Helsinki, Finland Phone: +358 9 191 25297 Fax: +358 9 191 25302 biswajyoti.sahu(a)helsinki.fi

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