- galaxy-user - lists.galaxyproject.org

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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incompatible frame
by Barbara Bryant 01 Jan '13

01 Jan '13

I'm having trouble viewing SeqPos output; I get "Please use a frames compatible browser when viewing this output" - yet I can see other frames in the browsers. Tried IE, Chrome, Firefox. Any suggestions? Thanks! This email message and any attachments are being sent by Constellation Pharmaceuticals, Inc. The information contained in this e-mail message, and any attachments, may contain information that is confidential or privileged. If you are not the intended recipient, any dissemination or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by return e-mail and destroy all copies of this message and any attachments. Thank you. For more information about Constellation, please visit us at http://www.constellationpharma.com.

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Pipeline design for bacterial RNA-Seq
by Bernardo Bello 01 Jan '13

01 Jan '13

Hi community, I have just discovered a wonderful Galaxy server for RNA-Seq analysis: Oqtans http://galaxy.raetschlab.org/. I am impressed by the huge quantity of useful tools that they have integrated there. I'm dealing with bacterial transcriptome analysis. We have the genome sequence of this bacteria. RNA samples are now been sequenced and I am designing a pipeline for data analysis. I would like you to suggest me the tools that I can/should use in order to analyse my data. My sequences come from Ion Torrent platform. For each sample I have a fastQ file of about 3 million sequences. They are less than 200 bp and have a mean of 150 bp. I you need more information please ask me. Thank you very much for your help. Regards, Bernardo -- *Bernardo Bello Ortí* PhD student CReSA-IRTA Campus de Bellaterra-Universitat Autònoma de Barcelona Edifici CReSA 08193 Bellaterra (Barcelona, Spain) Tel.: 647 42 52 63 *www.cresa.es * * *

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running out of disk space in cloudman instance
by Siddhartha Basu 30 Dec '12

30 Dec '12

Hi, The instance ran out of space very quickly as soon as i import ~4 3GB fastq file. The problem turns out to be identical as described here ... http://gmod.827538.n3.nabble.com/Re-galaxy-user-Problem-using-Galaxy-on-the… Is there any permanent fix available that is already baked into the entire cloud setup and workflow. For the time being, i circumvent the issue by mounting the /tmp in a separate ebs volume partition(~50GB), adding it in /etc/fstab and then reboot the machine. However, the /tmp has to be mounted without *noexec* option since the upstart python script executes another python script(cm_boot.py possibly) from /tmp to start the cloudman webapp. thanks, -siddhartha

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galaxy cluster nodes from the cloudlaunch site
by Sun, Wenping [USA] 27 Dec '12

27 Dec '12

Dear Galaxy users, I created galaxy instance using galaxy ami the first time. When I re-launch via cloudlaunch site the 2nd time, I have question on adding cluster nodes. There are several pull-down options for the nodes type, no matter which type I choose, they always generate nodes with only 15gb. Is there other option I can have option to define the root space for the nodes? Thank you, Kathryn

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