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?
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.
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.
My attempts to build a new custom genome failed on the public server
today, with a 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.
Michael J. Axtell, Ph.D.
Dept. of Biology
Penn State University
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
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
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
Thanks for any help!
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
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
>From run 1:
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:
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
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.
Michael J.G. Milevskiy | BBiomedSc
School of Chemical and Molecular Biosciences
Prof. Melissa Brown - Group Leader
Molecular Biosciences Building 76-432
The University of Queensland | (07) 3365 4635
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:
and to save some money on your registration, go to
before March 21 to register.
If you'd like to give a talk at the meeting please let me know.
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research