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

Download multiple files from history
by Adhemar 02 May '12

02 May '12

Hi, I'm trying to download multiple files from a given history but I couldn't figure out how to do it. Is there a way? Thanks, Adhemar

5 4

question about uploading data through URL method
by Xiangming Ding 20 Mar '12

20 Mar '12

Hi galaxy I am a new user of galaxy. i met a problem and didnot find similar question in FAQ. I wanted to upload the data from DDBJ DRA dataset to galaxy through UTL method. The file is around 800M. However after uploading, the FASTQ file was just around 2M. So I wanted know whether it is possible to upload a large file to galaxy through URL method? or I should download the file to my pc and then uploading to galaxy through FTP method. Thanks xiangmimg

6 19

Re: [galaxy-user] [galaxy-bugs] GI errors in the megablast table of results ?
by Guru Ananda 01 Mar '12

01 Mar '12

Dear Sandrine, Thanks for pointing out this issue. The BLAST databases we have on Galaxy are from last year, while those on NCBI website are the latest (Jan 2012). As pointed out on NCBI website ( http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html) it appears that each time any change is made to a sequence/database, GI numbers change as well. This is perhaps why you're observing discrepancies in GI numbers and lengths between megablast outputs on Galaxy and NCBI. I'm currently in the process of downloading the latest BLAST databases from NCBI, and I'll let you know when they're available for use on Galaxy. Thanks for your patience, Guru Galaxy team. On Wed, Nov 9, 2011 at 8:03 AM, Sandrine Hughes <Sandrine.Hughes(a)ens-lyon.fr > wrote: > Dear all, > > I’m not sure where I need to send my email so I apologize if I’m wrong. > > I have a trouble with the Megablast program available in NGS Mapping and I > hope that you can help. Indeed, I think that there might be a problem with > the table given in output, and notably a shift between the GI numbers and > the parameters associated. > > Here are the details: > > I. First, what I have done : > I used the program to identify the species that I have in a mix of > sequences by using the following options: > Database nt 27-Jun-2011 > Word size 16 > Identity 90.0 > Cutoff 0.001 > Filter out low complexity regions Yes > I run the analyses twice and obtained exactly the same results (I used > the online version of Galaxy, not a local one). > > II. Second, I analysed the data obtained for one of my sequence (1-202). > The following lines are the beginning of the table that I obtained after > the megablast and two lines with troubles: > > 1-202 312182292 484 99.33 150 1 0 1 > 150 1 150 2e-75 289.0 > 1-202 312182201 476 99.33 150 1 0 1 > 150 1 150 2e-75 289.0 > 1-202 308228725 928 99.33 150 1 0 1 > 150 19 168 2e-75 289.0 > 1-202 308228711 938 99.33 150 1 0 1 > 150 22 171 2e-75 289.0 > 1-202 308197083 459 99.33 150 1 0 1 > 150 10 159 2e-75 289.0 > 1-202 300392378 920 99.33 150 1 0 1 > 150 10 159 2e-75 289.0 > 1-202 300392376 918 99.33 150 1 0 1 > 150 9 158 2e-75 289.0 > 1-202 300392375 922 99.33 150 1 0 1 > 150 11 160 2e-75 289.0 > 1-202 300392374 931 99.33 150 1 0 1 > 150 21 170 2e-75 289.0 > 1-202 300392373 909 99.33 150 1 0 1 > 150 21 170 2e-75 289.0 > 1-202 300392371 1172 99.33 150 1 0 1 > 150 9 158 2e-75 289.0 > ... > 1-202 179366399 151762 98.67 150 2 0 1 > 150 46880 47029 6e-73 281.0 > 1-202 58617849 511 98.67 150 2 0 1 > 150 21 170 6e-73 281.0 > > > III. Third, what I’ve noticed: > My first trouble was that among all the species identified, two were > very different from the expected ones (2 last lines). So I decided to > search if that could be possible for that sequence and performed > independently a megablast on the NCBI with similar options. I was not able > to find these two species in the results. > So, I decided to check the hits identified in the table above and > identified a second trouble. In the table, the second column give the GI of > the database hit and the third column give the length of the database hit. > However, when I manually checked in NCBI the length of the GI, this one was > incorrect. Indeed, for the GI 312182292, the length should be 580 and not > 484. > By checking different lines, I noticed that the length that is given > for a GI corresponds to the length of the GI-1. As you can see in the above > table, some GI are consecutive (300392376, 300392375,...). When checking > the length of 300392376 in NCBI, I should have 920. But when I checked > 300392375, I found 918. And this was true for the following lines : > 300392374 give normally 922 and 300392373 give 931... My conclusion at that > point was that there was a shift of –1 between the GI and the other > parameters of the line (indeed the parameters for the remaining columns are > in agreement with the length of the GI-1). However, that’s not always > true.... For some GI given in the table (for example, the two last lines), > if we check the parameters of the GI-1, the parameters are completely > different... So, I suppose that there is a trouble in the GI sorting during > the megablast but I’m not able to clearly define the problem. > > IV. Fourth, confirmed with an other dataset > In order to be sure that the problem was not linked to my data or my > process, I asked a colleague to do a megablast on independent data. The > conclusions were similar to mine : a shift in the GI given in the table > and the parameters associated, that most of the time but not always, > correspond to GI-1. > > Can you confirm that there is a problem with the output of the megablast > available in Galaxy ? If yes, do you think you can fix it ? > > Many thanks for your help, > > Best regards, > > Sandrine > -- Graduate student, Bioinformatics and Genomics Makova lab/Galaxy team Penn State University 505 Wartik lab University Park PA 16802 guru(a)psu.edu

2 1

SamTools Filter Pileup "Only report variants?" option is misleading
by Jesse Erdmann 08 Feb '12

08 Feb '12

In using the filter pileup tool we've discovered that the option "Only report variants?" will throw away lines that have indels provided that they do not contain any SNPs. For example the line: chr1 88427041 C 38 ..+1A..+1A.....+1A.,..+1A.....,.+1A,.,......,...,^~.^~,^~,^~, HHHHHFEHHHHHBFHHHHHHBFHHHEHHHAHHHFHG#E will not be included in the filtered results. At the very least we would recommend relabeling the option to "Only report SNP variants?" But it would also be helpful to include an option to filter for both SNP and indel variants. Thanks! -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann(a)umn.edu 612-626-3123

2 1

Re: [galaxy-user] Disk Quote
by Zack Liu 07 Feb '12

07 Feb '12

Dear galaxy admins, I am working on a hi-seq project, where each file is ~ 50G. I have 8 of them. After I uploaded my files, I realized that I have reach my quote limit. Literally, I can't do any mapping or actions on these files since I have no disk space for it. I was wondering if there's anyway I can get more disk storage on galaxy. Thanks! Zack Liu

2 1

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/

1 0

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

2 1

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

2 1

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...

3 5

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

4 8