March 2013 - galaxy-user - lists.galaxyproject.org

Do I need to specify the file format when I upload datasets using FTP method?
by Du, Jianguang 21 Mar '13

21 Mar '13

Hi Everyone, When I upload my datasets onto my history via FTP method (using FileZilla), do I need to specify the file format under "File Format" of "Upload File from your computer"? I noticed that the screencast of how to upload datasets via FTP just leaves the "File Format" as "Auto-detect". However, I also noticed this sentence in the help for Auto-detect: "the system will attempt to detect Axt, Fasta, Fastqsolexa, Gff, Gff3, Html, Lav, Maf, Tabular, Wiggle, Bed and Interval (Bed with headers) formats". Do I need to specify the format of my datasets if the format of my datasets is not listed in the sentence above? Thanks. Jianguang

2 1

Galaxy Main jobs not running?
by Nicole Cloonan 20 Mar '13

20 Mar '13

Hello, I was just wondering whether anyone could confirm whether the Galaxy Main server is currently under heavy load, or whether there is some other problem with job dispatch? I have not been able to successfully run any jobs today. Thanks! Nicole.

2 2

Problem with workflow step ordering
by Ian Donaldson 19 Mar '13

19 Mar '13

When i create a GALAXY workflow the order of the steps in the summary are fine until the main pipeline diverges into multiple branches. Then the steps from the different branches get shuffled in the summary and it is difficult to see what is going on. Q. Is it possible to manually reorder steps in a GALAXY workflow summary? There used to a problem where workflows with multiple inputs would randomise the order of the inputs each time the workflow was run. Now the proximity of the inputs to the top left-hand edge of the workflow dictates the precedence. Also, if i manually run the steps one at a time in order in a history and create a workflow from that, in the creation summary (just before making the workflow) everything is in order, however when the workflow is run the order has been messed up. Thanks, Ian

2 1

Server error during custom build on main
by Michael Axtell 19 Mar '13

19 Mar '13

Hello, My attempts to build a new custom genome failed on the public server today, with a server error .. "Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)" I checked md5 of the fasta file which I was building and it was fine, pretty sure the .len file was OK too. No job ever starts .. server error is returned very quickly. Any advice would be appreciated, thanks in advance. - Mike -- Michael J. Axtell, Ph.D. Associate Professor Dept. of Biology Penn State University http://axtell-lab-psu.weebly.com

2 3

Medicago and Soybean Genome in Galaxy
by Oswaldo Lopez 19 Mar '13

19 Mar '13

Hi my name is OswaldoI would like to analyse my RNAseq data from Medicago truncatula and soybean samples on Galaxy. However, the genome of these legumes are not listed on Galaxy, is there a way to get these genomes on Galaxy? Thanks very much Oswaldo

2 1

Galaxy LinkedIn Group
by Dave Clements 18 Mar '13

18 Mar '13

Hello all, A Galaxy Group now exists on LinkedIn <http://bit.ly/gxyLinkedIn> ( http://bit.ly/gxyLinkedIn) The group is open to anyone and is a forum to post announcements, discussions <http://bit.ly/gxyLinkedIn>, and jobs of interest<https://www.linkedin.com/groups?jobs=&gid=4907635&trk=anet_ug_jobs> to the Galaxy community. *Note that this is not an official support forum for the Galaxy Project. Please continue to use the mailing lists<http://wiki.galaxyproject.org/MailingLists> for that purpose.* If you are on LinkedIn, please consider joining the group<http://bit.ly/gxyLinkedIn> today. Dave Clements <http://wiki.galaxyproject.org/DaveClements> and the Galaxy Team <http://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

1 0

Importing archived Histories
by Clare Sloggett 18 Mar '13

18 Mar '13

Hi all, I have some previously exported Histories saved as files. I want to import them to Galaxy but I can't work out how. I suspect I'm missing something basic! When I go to the History panel drop-down menu and select 'Export to File', I get a downloaded tar.gz file. When I select 'Import from File', I get a text box that asks me for the Archived History URL. But, I don't have a URL - I have a file on my local machine which I got by exporting as above. I have been able to import Histories directly from running Galaxy instances, by the way, I just can't work out how to do it from a file. Since it's possible to export them to a file in the first place, I am guessing that there's a way to import them too? I noticed that the forms for importing Histories and importing Workflows (.../workflow/import_workflow) are different in that the Workflows version explicitly asks for either a URL or for a local file. So, I have been able to successfully import Workflows from json files, but am confused about Histories. Thanks for any help! Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759

2 1

Cuffdiff statistical calculations are inconsistent?
by Jenna Smith 15 Mar '13

15 Mar '13

Hi, I'll preface my concern by saying that I'm a novice to Cufflinks. Back in September, I performed a Cuffdiff analysis comparing a wild-type and mutant condition. The analysis returned ~800 transcripts differentially regulated between the two with statistical significance. Recently, I've rerun the Cuffdiff analysis - using exactly the same files stored in Galaxy for all inputs, and with all the same parameters - and only get a few dozen statistically significant hits. However, all of the data besides the p and q values are essentially identical between these two runs, so I am really unclear as to what is causing the difference. Here is just one clear example: >From run 1: YFR026C FPKM 1 = 17.2434 FPKM 2 = 196.735 log2(fold change) = 3.51214 p = 1.64E-8 q = 7.33E-6 significant = yes >From run 2: YFR026C FPKM 1 = 14.4489 FPKM 2 = 144.939 log2(fold change) = 3.32641 p = 0.000170034 q = 0.0719964 significant = no The second Cuffdiff analysis shows there is still a ~10-fold difference between conditions, but this is not statistically significant. Has the version of Cuffdiff on Galaxy been updated such that some parameters have changed, that could explain this difference? Or, is there some setting I am missing that would cause very large changes to fail statistical significance testing? Any help or input would be appreciated, I am really at a loss for why executing what should be exactly the same task is giving vastly different results. I could just be overlooking something very fundamental that is obvious to someone with more experience with this program. Thanks. -Jenna Smith

3 4

How to connect to private instance of galaxy from another computer
by Michael Milevskiy 14 Mar '13

14 Mar '13

Dear Galaxy, I am running an instance of Galaxy on my computer through localhost:8080/ and am wondering if I can use this on my laptop? I basically don't want to be at the computer at the same time and don't want to upload files to and from my laptop but just use the galaxy interface to work with my data. Regards, Michael J.G. Milevskiy | BBiomedSc PhD Student School of Chemical and Molecular Biosciences Prof. Melissa Brown - Group Leader Molecular Biosciences Building 76-432 The University of Queensland | (07) 3365 4635

2 1

Early registration for GMOD meeting closes in one week
by Scott Cain 13 Mar '13

13 Mar '13

Hello, The GMOD meeting is in Cambridge, England on April 5-6 (right before the Biocurator meeting) and early registration closes March 21 (in one week). It is shaping up to be a good meeting with several interesting talks scheduled. Please try to make it! For more information on the meeting, see the meeting page: http://www.gmod.org/wiki/April_2013_GMOD_Meeting and to save some money on your registration, go to http://gmod2013.eventbrite.com/ before March 21 to register. If you'd like to give a talk at the meeting please let me know. Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

1 0