- galaxy-user - lists.galaxyproject.org

The size of the history
by 杨继文 02 Feb '12

02 Feb '12

Hi all, First I would like to thank you for your fast replies to my questions. As you know, at top right corner of Galaxy window, there are records of the history size and how many percentage of memory space has been used. I found that the number in the records only increases, but doesn't decrease after I delete files permanently. DId I miss something? How to let the record show the real size of the histories? Thanks in advance. Greetings, Jiwen

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FTP and Biomart
by 杨继文 01 Feb '12

01 Feb '12

Hi All, Today I have problem to use FTP to upload data to Galaxy. I used Filezilla software and the server name "main.g2.bx.psu.edu", but I can not connect to the server. Something wrong with my operation? Also, when I tried to get data from Biomart to Galaxy, I got the error warning "the uploaded file contains unappropriate HTML links " Hope you can tell me if I did something wrong. Thanks Jiwen

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A simple operation didn't work out
by 杨继文 01 Feb '12

01 Feb '12

Hi All, I got a bit disappointed when I failed in the following operation which seems to be simple. I uploaded mouse annotation/reference gene sets (GTF format) to Galaxy. The file is located at ftp://ftp.ensembl.org/pub/release-65/gtf/mus_musculus/. As far as I know, GTF file is tab delimited, thus I used "Filter and Sort" --"filter" With following condition:C1 == 19 . column 1 is where chromosomes are located. I want to pick up all lines which belong to chromosome19. However, I only got an empty file. I know this is not a bit issue to discuss here. But I still hope you can help me figure out what 's wrong. Thanks Jiwen

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clustering algorithm in Galaxy
by Daniel Elleder 01 Feb '12

01 Feb '12

Is there a good read clustering algorithm available in Galaxy? Specifically for 454 and Ion Torrent reads. In the Galaxy e-mail archive I see mentions of dnaclust, but I cannot find it in the menus.

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February 2012 Galaxy Update
by Dave Clements 01 Feb '12

01 Feb '12

Hello all, The inaugural edition <http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02> of *Galaxy Update <http://wiki.g2.bx.psu.edu/GalaxyUpdates>* is now available. *Galaxy Update <http://wiki.g2.bx.psu.edu/GalaxyUpdates>* is a (mostly) monthly summary of what is going on in the Galaxy community. *Galaxy Updates* will complement the *Galaxy Development News Briefs<http://wiki.g2.bx.psu.edu/DevNewsBriefs> * which accompany new Galaxy releases and focus on Galaxy code updates. *Highlights:* - New Papers <http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#New_Papers> - New Public Server: MGTAXA<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#New_Public_Server:_MGTAXA> - Open Positions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#Who.27s_Hiring> - Upcoming Events and Deadlines<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#Upcoming_Events_and_Deadlin…> - GCC2012 Sponsors<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#GCC2012_Sponsors> - New Distributions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#New_Distributions> If you have anything you would like to see in the March *Galaxy Update*, please let me know. Dave Clements Link: http://galaxyproject.org/wiki/GalaxyUpdates/2012_02 -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Gene and transcript names from Cuffdiff
by 杨继文 01 Feb '12

01 Feb '12

Hi all, I am learning how to use Galaxy to analyze my RNA-Seq data. After running cuffdiff, one of the files I got is "transcript differential expression testing". In this file, I can see " gene_id" is something like "XLOC_000001". I am wondering how I can find the name of differentially expressed genes and transcripts. Can anyone help me?????? Thanks in advance. Jiwen

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Server Error when running workflow
by Stephen Eacker 01 Feb '12

01 Feb '12

Hello, I'm using Galaxy main to run some workflows. I'm running into a "Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)" when running my workflow. I've seen that a number of others in the Q&A archives have had similar problems that were resolved by patches. Steve Stephen Eacker, Ph.D. Postdoctoral Fellow Dawson Lab Institute for Cell Engineering Johns Hopkins Medical Institute (443) 287-5605 seacker1(a)jhmi.edu

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Error during data upload of fastq.gz
by Stefan Kroeger 31 Jan '12

31 Jan '12

hi, Maybe anybody can give me a hint for the following problem... When I try to upload a fastq.gz file into galxy using url function the input os canceled with the following exception: An error occurred running this job: The uploaded file contains inappropriate HTML content I don't know where to start to have a look at. The upload of all other fastq.gz files from the same run works smooth. best stefan PS. Yes I know, the problem is really unspecific, sorry for that...

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CloudMan Web Launcher / BioCloudCentral - Not showing public DNS
by mailing list 31 Jan '12

31 Jan '12

Hi guys, When I launch using BioCloudCentral (http://biocloudcentral.herokuapp.com) I noticed it doesn't show my public DNS. Even if I wait for a few minutes. For the "Public IP (Cloudman Console)" table cell, it just shows blank, and for the SSH access area is just says "ssh ubuntu@" It hasn't been a big deal because I just pull it from my EC2 console. But now I'm writing up some documentation for other researchers to use our application running on CloudMan, and it adds a lot of complexity to the documentation to tell them to log into the EC2 console, click on instances, copy the public DNS ... It would be excellent if they could just click a link from the launch page! Let me know if I can help with debugging. Thanks again, Greg

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Walltime exceeded
by Hemarajata, Peera 31 Jan '12

31 Jan '12

Dear all, My Cufflinks jobs keep getting killed due to the walltime limit. Is there a way to fix this or is there anything I can do to reduce the size of my BAM datasets so the analysis can get done? Thank you! Peera Hemarajata

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