gmane.science.biology.galaxy.user

Re: (no subject)

Jennifer Jackson — 2013-05-20T23:30:01

Hi Giuseppe,

Data has to be local to the instance you are working on in order to use 
it. You can move individual datasets by downloading/uploading them. And 
move entire histories using the menu above the history panel and the 
options "Export to File" and "Import to File".

Best,

Jen
Galaxy team

On 5/20/13 4:10 PM, Ianiri, Giuseppe wrote:

Re: changing parameters in tophat

Jennifer Jackson — 2013-05-20T23:12:36

Hello,

On the Tophat tool form, if you scroll to the very bottom, the list of 
implemented option is listed. In general, the order will be the same as 
the options on the form.

*     Tophat parameter list*
      This is a list of implemented Tophat options:

    -G/--GTF [GTF 2.2 file]           Supply TopHat with a list of gene model annotations. TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping.
    -j/--raw-juncs [juncs file]       Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-], left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive.
    -no-novel-juncs                   Only look for junctions indicated in the supplied

(no subject)

Ianiri, Giuseppe — 2013-05-20T23:10:49

Hi,
I have worked so far on the free web-based version of Galaxy; now I have installed Bio-Linux 7, and there is Galaxy in there as well. However, I cannot access to my data (stored on the web version of Galaxy) using Galaxy on Bio Linux. If it is possible, does anyone know how to do it?
Thanks,


Giuseppe Ianiri

changing parameters in tophat

Colaneri, Alejandro Cesar — 2013-05-20T21:38:35

I want to run tophat with the parameter  "--no-novel-juncs genome"
Where do I find the options to add this parameter?
Dr. Alejandro Colaneri
Departments of Biology
University of North Carolina at Chapel Hill
310 Coker Hall, CB# 3280
120 South Road
Chapel Hill, NC 27599-3280
Tel: 919-962-2273
fax: 919- 962-1625

Re: User -> Custom Builds fail on public server

Michael Axtell — 2013-05-18T00:13:15

Thanks Jen.  Sigh.  I tried a few more times of the course of the
afternoon, no luck.  It's been several days now.  Anyway, thanks for
letting me know its related to usage on Public-Main.

Mike



On Fri, May 17, 2013 at 4:21 PM, Jennifer Jackson <jen-dukY5rQBki03uPMLIKxrzw< at >public.gmane.org> wrote:

Re: Raw counts from Galaxy

Jennifer Jackson — 2013-05-17T22:41:45

Hello Els,

For initial versions, the RNA-seq pipeline's tool authors did not 
provide any counts of this type (on purpose). The latest version does 
include a type of count (alternate to the normalized FPKM counts) and it 
is described at the Cufflinks web site, under the tool Cuffdiff -> Count 
Tracking. This is not yet incorporated into Galaxy.
http://cufflinks.cbcb.umd.edu/faq.html#numfrags
http://cufflinks.cbcb.umd.edu/manual.html

If your reads are mapped a reference genome, and you have transcripts 
mapped to the same reference genome, you can compare the overlapping 
coordinates and generate counts. This will assign reads to more than one 
transcript - "raw" counts based only on overlap. Tools to use for this 
purpose can be found in the group "BEDTools" or you could covert the 
SAM/BAM alignments to interval format and use the tools in " Operate on 
Genomic Intervals" and the tool "Group" as needed.

Hopefully this helps,

Jen
Galaxy team

On 5/17/13 2:11 AM, Els Willems wrote:

Re: failed Tophat processing steps

Jennifer Jackson — 2013-05-17T22:13:53

Hi Nikolay,

If you click on one of the red dataset's names, more information will be 
given in that expanded view. If the error designates a cluster error, 
then yes, a re-run is the correct solution. If it is another type of 
tool error, then the root cause can be investigated (this is usually 
associated with inputs).

Some tips for trouble-shooting tool errors:
http://wiki.galaxyproject.org/Support#Error_from_tools

How to submit a bug report for error datasets that you would like 
help/feedback on:
http://wiki.galaxyproject.org/Support#Reporting_tool_errors

Transitory cluster issues are rare compared to the total volume of jobs 
processed, but they do occur and we apologize for the confusion that 
they can cause. Hopefully this info helps you to determine they type of 
error, or you can submit the bug report and we can give direct 
confirmation/feedback.

Best,

Jen
Galaxy team

On 5/17/13 2:26 PM, Nikolay N. wrote:

failed Tophat processing steps

Nikolay N. — 2013-05-17T21:26:10

Hi,

I submitted a sample for Tophat processing on the main Galaxy instance and
it seems to me that that the processing of that sample has failed. The
corresponding sections in the history are in red (see attached screenshot).

How can I find out what has happened? I don't see any error message.

Shall I simple re-submit these processing steps hoping that next time they
won't fail?

many thanks,

Nikolay

Re: User -> Custom Builds fail on public server

Jennifer Jackson — 2013-05-17T20:21:45

Hi Mike,

This warning is known to come up after executing certain functions right 
now on the public Main Galaxy instance. The situation is temporary and 
related to the current high usage load. I just tried this exact function 
and didn't get the warning, which reconfirms what we know (timing is a 
factor) and rules out other issues (a true problem with the function 
itself). Please try the function now, and if you run into the same 
warning, wait a few minutes, then try again. If it continues or becomes 
bothersome, consider waiting longer between attempts.

We are monitoring the usage load very carefully and doing our best to 
mitigate problems such as this one. If your work is very urgent during 
this peak usage time, a cloud Galaxy may be a good solution.
http://usegalaxy.org/cloud

Thank you for your patience,

Jen
Galaxy team


On 5/17/13 9:18 AM, Michael Axtell wrote:

Re: Duplicate Accounts on Main

Dave Clements — 2013-05-17T18:56:57

Dear Galaxy Community,

Thank your for your feedback regarding the removal of duplicate
accounts<http://wiki.galaxyproject.org/News/DuplicateAccountsOnMain>on
Galaxy Project's free Galaxy server,
http://usegalaxy.org (a.k.a. Main).

If you have already replied, please know that we are currently processing
your responses and feedback to terms_and_conditions-gv2aE17SRA+oClj4AeEUqwRtnQ8X5fEL< at >public.gmane.org Our
team will be responding shortly.

Whenever possible, please follow the instructions in the original email,
using the provided link to indicate the account you wish to retain. We have
given a 30 day window to download or move data out of duplicate accounts,
after that time they will be deleted, and there is no need to take
additional action.

Please note that this process is automated and will continue, and repeat
violation will result in permanent loss of access privileges. When moving
data, be sure to move it to the primary account you have indicated, and not
any duplicate accounts (existing or new).

User -> Custom Builds fail on public server

Michael Axtell — 2013-05-17T16:18:57

Hello.  For the last several days the Custom Builds dialog has failed
on the public server (main.g2.bx.psu.edu).  Specifically, User ->
Custom Builds returns the 'Internal Server Error' message, and other
paths to the custom builds tools similarly have been failing for me.
Advice?

Thanks!
Mike


--
Michael J. Axtell, Ph.D.
Associate Professor
Dept. of Biology
Penn State University
http://axtell-lab-psu.weebly.com

Re: receiving an email when a processing step finishes

Dannon Baker — 2013-05-17T13:56:05

Actually, you can do this in workflows out of the box in Galaxy (as long as
your instance is configured to send mail).

All you need to do is edit the workflow, select the step you want to be
notified following, and add a Step Action-> Email Notification.



On Fri, May 17, 2013 at 9:41 AM, Geert Vandeweyer <
geert.vandeweyer2-pPLrx3cd0hQ< at >public.gmane.org> wrote:

Re: receiving an email when a processing step finishes

Geert Vandeweyer — 2013-05-17T13:41:32

Hi,

Currently not. For local/cloud instances, you can install an extra tool 
for this from the toolshed:

http://toolshed.g2.bx.psu.edu/view/geert-vandeweyer/sendmail

best
geert

On 05/17/2013 03:01 PM, Nikolay N. wrote:

receiving an email when a processing step finishes

Nikolay N. — 2013-05-17T13:01:14

Hi,

I am using the main galaxy instance and have submitted several processing
steps that seem to have been scheduled for execution. Is there a way to get
an email notification when such a processing step finishes?

many thanks,
Nick

Raw counts from Galaxy

Els Willems — 2013-05-17T09:11:49

Dear all,



I would like to analyse some RNA-Seq I obtained in the chicken. I am implemented the Tophat-Cufflinks pipeline in Galaxy, but I would like to obtain a raw count of the number of mappings per transcript. I have not found a way to do this in Galaxy, is this possible? Thank you very much.



Regards, Els



---
Ir. Els Willems
KU Leuven
Department of Biosystems
Division Livestock - Nutrition - Quality
Laboratory of Livestock Physiology
Kasteelpark Arenberg 30 bus 2456
B - 3001 Heverlee
T (+32) 016 32 17 29
F (+32) 016 32 19 94

Re: Dataset does not appear in a drop-down menu of a tool

Jennifer Jackson — 2013-05-16T22:13:41

Hello,

Many tools that work with FASTQ inputs, including this one, require a 
dataset to be in ".fastqsanger" format. This wiki explains more about 
how to go from .fasta -> .fastasanger format (when necessary) and 
designating that format with the proper "datatype" assignment:
http://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset
See "Dataset special cases: FASTQ"

Hopefully this helps,

Jen
Galaxy team

On 5/16/13 2:31 PM, Nikolay N. wrote:

Dataset does not appear in a drop-down menu of a tool

Nikolay N. — 2013-05-16T21:31:07

Hi,

I just started using the main galaxy instance. I uploaded via FTP and
imported several FASTQ files. They all appear in the list of my "saved
datasets" (see attached screenshot). However, when I click on any of the
tools in the left panel (e.g. "FASTQ Summary Statistics") I get in the
middle panel the info for the tool but the dropdown menu listing the
available FASTQ files is empty (see attached screenshot). What do I need to
do to be able to perform analysis on the FASTQ files that I uploaded?

many thanks,

Nikolay

Duplicate Accounts on Main

Dave Clements — 2013-05-15T23:39:02

Hello all,

The terms of use <https://main.g2.bx.psu.edu/static/terms.html> for the
Galaxy Project's free Galaxy server, http://usegalaxy.org (a.k.a.
Main<http://wiki.galaxyproject.org/Main>)
specify

Your access to the Service is provided under the condition that you abide
by any published quotas on data storage, job submissions, or any other
limitations placed on the public Service. *Attempts to subvert these limits
by creating multiple accounts or through any other method may result in
termination of all associated accounts.*


In the past we have dealt with multiple accounts on an ad-hoc basis.
 Moving forward we are using an automated system to detect, disable, and
eventually delete duplicate accounts.  If the automated system determines
that your account is a duplicate, your account will be disabled and you
will receive an email asking you if this is the account you wish to keep.
 If it is, please follow the directions in the email and your access to
that account will be restored.

If your account is s

Re: [External] Re: Question on galaxy data visualization

Sun, Wenping [USA] — 2013-05-14T17:56:26

Jen,
Thanks for the information.
Kathryn

From: Jennifer Jackson [mailto:jen-dukY5rQBki03uPMLIKxrzw< at >public.gmane.org]
Sent: Monday, May 13, 2013 6:18 PM
To: Sun, Wenping [USA]
Cc: galaxy-user-btkOtGxnL5087WB9TwDe4A< at >public.gmane.org
Subject: [External] Re: [galaxy-user] Question on galaxy data visualization

Hello Kathryn,

Trackster is the primary data visualization tool and can be accessed by clicking on the mini graph icon within a dataset:

[cid:image001.png-M16tkalm5QkdA8cXb8820DRmByFHzeGd< at >public.gmane.org]

or by going to "Visualization" in the upper menu bar and starting a new track browser.
http://wiki.galaxyproject.org/Learn#Visualization

If you are interested, for certain datasets, the icon will also offer other options: Circster and/or Scatterplot. The tool group "Graph/Display Data" has graphing tools and tools that prepare data to be visualized. The tool group "Motif Tools" has a sequence logo generator, and the groups " NGS: QC and manipulation" and " BEDTools" have more graphing tools.

Hopefu

Re: problem uploading txt data

Chunyu Liu — 2013-05-14T17:26:22

Thanks! for fixing the problem before I get time to provide more test data.

Chunyu


On Tue, May 14, 2013 at 12:17 PM, Daniel Blankenberg <dan-dukY5rQBki03uPMLIKxrzw< at >public.gmane.org> wrote:

Re: problem uploading txt data

Daniel Blankenberg — 2013-05-14T17:17:47

Hi Chunyu,

Thanks for reporting this issue, it has been resolved in our stable branch and will be available on our public server after the next update.


Thanks for using Galaxy,

Dan


On May 12, 2013, at 10:52 AM, Chunyu Liu wrote: