October 2012 - galaxy-user - lists.galaxyproject.org

from Galaxy to Megan
by Judith van Bleijswijk 10 Oct '12

10 Oct '12

Dear Galaxy users that also use Megan, I hope you can help me combining Galaxy with Megan4. I followed the Galaxy metagenome workflow (author aun1) on shotgun DNA 454 sequences of two samples that I would like to compare. The results are two nice trees and tables with the lowest taxonomic ranks for the two samples. Besides the taxonomy I am also interested in the functions and I would like to use Megan4 (with SEED and KEGG classification) for this purpose. I tried to import a Galaxy file (.tabular) with c1 =high quality segment name and c2-c13 =blasthit results and a Galaxy fasta file with the high quality segment names and sequences. This does not work and I receive the message parsing failed, no reads found. I am interested to know how you solved this issue and which files in the Galaxy metagenome workflow you use to import into Megan4. Or maybe there is other software that you use to compare suits of functional genes in your metagenome datasets? Regards, Judith van Bleijswijk

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Galaxy not showing my reference genome in Drop down for BowTie
by greg 10 Oct '12

10 Oct '12

Hi guys, As shown in the attached screenshot I uploaded a fasta file. And I want to use it as my reference genome for running bow tie but it doesn't appear in the dropdown on the bow tie tool. I'm sure I'm missing something obvious. Thanks, Greg

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Why doesn't bowtie in galaxy accepting colorspace reads directly?
by Praveen Raj Somarajan 09 Oct '12

09 Oct '12

Hi All, I'm wondering why the Bowtie version in (even latest) Galaxy does NOT support .csfasta/.qual input files directly, though it is mentioned under "Map with Bowtie for SOLiD". This is the case of "BWA for SOLiD" as well. One would expect direct support on colorspace files. Do you have any plans of implementing this?I see this would be a great support to SOLiD users. Look forward to your comments Thanks, Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

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galaxyTools volume not given enough time to attach
by Joel Rosenberg 09 Oct '12

09 Oct '12

About half the time I try to boot up my galaxy cluster in AWS, cloudman aborts because it could not attach the galaxyTools volume with the line: "Cannot attach volume 'vol-xxxxxx' in state 'creating' It appears that in /cm/services/data/volume.py it tries to mount the volume every two seconds up to a minute and then gives up. In the AWS EC2 volume pane, the volume in question always eventually ends up in the state "available", but often not in enough time and cloudman gives up. Could you possibly 1) increase the timeout to account for variations in AWS service performance, 2) selectively wait longer if the state is "creating" or 3) make the timeout period configurable in galaxy's settings? If it matters, the tools snapshot is my own that I made after modifying the standard volume. But again, when it boots up successfully the other half of the time, the cluster behaves normally. Thanks, Joel

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genome-wide Bisulfite analyses ... was Re: Infinite TopHat run
by Björn Grüning 08 Oct '12

08 Oct '12

Hi David, please do not hijack a different thread :) If you are analysing Bisulfite data i would recommend to have a look at http://www.bioinformatics.babraham.ac.uk/projects/ ... especially at bismark. We have written a wrapper for bismark, its still in testing phase but if you like to try it out, you are welcome. Cheers, Bjoern > Hi, there, > > I just got two genome-wide Bisulfite sequences from BGI and start to > analyze the data. > > I am trying to use Galaxy; but I find there is no such platform > available. Does anybody know where I can find this kind platform at > Galaxy or other places. > > Thanks > > David >

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RNA-seq analysis withtout reference genome
by Alicia R. Pérez-Porro 08 Oct '12

08 Oct '12

Hi all, I'm about to start doing gene expression analysis but i don't have a reference genome. I got my sequences from Illumina and i did my assemblies with CLC bio. I was planning to use DESeq for the analysis but for that i need my gene expression count values. There is any tool in Galaxy that i can use for that? Thanks, Alicia. –– Alicia R. Pérez-Porro PhD student Giribet lab Department of Organismic and Evolutionary Biology MCZ labs Harvard University 26 Oxford St, Cambridge MA 02138 phone: +1 617-496-5308 fax: +1 617-495-5667 www.oeb.harvard.edu/faculty/giribet/

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Infinite TopHat run
by Jonsson, Philip 08 Oct '12

08 Oct '12

I am running Galaxy online, excuting TopHat on a fastq file, something which I previously have done without problems. This time, my data file is maybe double the size and does not seem to ever get done (I'm on the fourth day or so). Previously I have never experienced that this has taken more than 24 hrs. Any idea what could be going on? /Philip

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Data Limit
by Mark Lindsay 08 Oct '12

08 Oct '12

Despite clearly all my files and histories, the history is red (using 100%) and stating 'You are over your disk quota'. Is there a way to remedy this situation? Mark

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data expiration policy
by Hiram Clawson 08 Oct '12

08 Oct '12

Good Morning Galaxy Universe: What is the data expiration policy at Galaxy for user created big* files that are then subsequently used in custom tracks at UCSC ? We are noticing users with bigDataUrl paths of: https://main.g2.bx.psu.edu/display_application/.../somefile.bigwig which appear to be expiring. The UCSC users have these tracks saved in UCSC sessions expecting the data to live as long as their session. I note when I attempt to access this type of https URL, it says: ERROR: certificate common name `bigsky.bx.psu.edu' doesn't match requested host name `main.g2.bx.psu.edu'. And if I alter main.g2 to be bigsky.bx.psu.edu, the returned information says: "This dataset has been deleted, you cannot view it at an external display application." --Hiram

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How to do an GO enrichment analysis in Galaxy?
by Yan He 08 Oct '12

08 Oct '12

Hi everyone, I got a list of differentially expressed genes from my RNA-seq data. Is there a tool on Galaxy that I can do the GO enrichment analysis for the differentially expressed genes? Any help or suggestion is highly appreciated! Best regards, Yan

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