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

Help with Summary Statistics
by D. A. Cowart 23 May '14

23 May '14

Hello, I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been organized and sorted by species. The format of the data is as follows: >HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC >HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT etc...for each species I have attempted to use the "Summary Statistics" button, however it appears to only be for numerical data and not sequence data. Is this tool/task available via Galaxy? Thank you, Dominique Cowart User name: dac330

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SNP finding
by Xiefan Fang 03 Dec '13

03 Dec '13

Dear galaxy users, We have done deep sequencing on some known genomic loci using Hiseq2000. I have already mapped the reads to the reference sequences by using Galaxy. In the next step, I want to find SNPs and calculate the SNP percentage within the reads. There are 500,000 to 1,000,000 reads per biological sample. Can I do it with galaxy? If not, is there other programs available in windows? Considering that I am not very familiar with programming. Thanks, Xiefan University of Florida

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extracting a subset of sequences from a very large fasta file(1.5 million)
by Perumal Vijayan 15 Feb '13

15 Feb '13

I have successfully uploaded a large fasta file (2.5 million genomic sequence contigs) onto Galaxy server. I wish to extract a subset of sequences from this file. I have a list of the fasta headers. Is there a way I can accomplish this on Galaxy? -- Perumal Vijayan Saskatoon Canada

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Nominate topics for the 2013 Galaxy Community Conference (GCC2013) Training Day
by Dave Clements 07 Jan '13

07 Jan '13

Hello all, Nominations are now open <http://bit.ly/gcc2013nom> for Training Day topics<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay>at the 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013>. GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> will start on 30 June with a Training Day featuring 4 parallel tracks, each with three, two hour workshops, for a total of twelve sessions. Any topic of interest to the Galaxy Community can be nominated<http://bit.ly/gcc2013nom>(see what was offered at GCC2012<http://wiki.galaxyproject.org/Events/GCC2012/TrainingDay>). Topics can be repeats from last year or brand new, and you are encouraged to nominate as many topics as you like. The 2013 Galaxy Community Conference (GCC2013) <http://wiki.galaxyproject.org/Events/GCC2013> will start on 30 June with a Training Day featuring 4 parallel tracks, each with three, two hour workshops, for a total of twelve sessions. Nominations will be compiled into a uniform list, and then topics will be voted on by the Galaxy Community starting in late January. Topic nomination closes 11 January. Thanks, Dave Clements, on behalf of the GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers#Organizing_Committee> Links: http://bit.ly/gcc2013nom - nominate a topic http://bit.ly/gcc2013td - Training Day page http://galaxyproject.org/GCC2013 - Conference home page http://bit.ly/gcc2013prom - help get the word out -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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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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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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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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