On Wed, Apr 20, 2011 at 4:00 AM, Edward Dudley wrote:
> Hi -
>
> I have a set of 454 reads that have been trimmed and converted to BAM format
> using Galaxy, and I can visualize the alignment with E. coli genomes using
> the UCSC browser. Problem is, I'd like to display the alignment in Artemis,
Are you downloading the ³BAI² index file, as well?
That might be the problem.
Best,
Ann
On 4/19/11 11:00 PM, "Edward Dudley" wrote:
> Hi -
>
> I have a set of 454 reads that have been trimmed and converted to BAM format
> using Galaxy, and I can visualize the alignment with E. coli genomes
Hello,
I posted to the seqanswers forum, but have not received any feedback. I am
working with RNA-seq Illumina data files in Galaxy
(http://main.g2.bx.psu.edu/). The two files are 100bp paired-end reads,
multiplexed with barcoding to distinguish samples. The barcodes are the first
four bases
Hi all,
I noticed a new problem with our local Galaxy (recently updated),
but found it happens on the public installation too.
I can edit workflows, and create run time parameters like ${Name}
or ${Name with spaces}, but when I come to run the workflow I get
an error:
> Server Error
>An error o
The issue you're seeing is actually related to improper initialization of the
workflow parameters index in the special case where a particular parameter is
only used in a rename action and not in a tool step. This is fixed in revision
5400:6cacf178a129.
-Dannon
On Apr 20, 2011, at 10:28 AM,
On Wed, Apr 20, 2011 at 3:44 PM, Douglas Allan
wrote:
> get me off this email list
>
Please don't hijack existing threads.
See:
http://lists.bx.psu.edu/pipermail/galaxy-user/2011-April/002281.html
and:
http://lists.bx.psu.edu/pipermail/galaxy-user/2011-April/002439.html
Peter
_
Hi Dan,
On Wed, Apr 20, 2011 at 3:47 PM, Dannon Baker wrote:
> The issue you're seeing is actually related to improper initialization of
> the workflow parameters index in the special case where a particular
> parameter is only used in a rename action and not in a tool step. This
> is fixed in r
Hi,
I've followed this thread with interest. I have had a problem on one of my
workflows, it fails to perform a sort on a dataset returning the error "sort:
invalid number at field start: invalid count at start of `None,Nonen'".
However, this error makes no sense. When I ask it to run the job a
I'll take a look at the workflow in question, if you'd like to share it with me
at this email address, 'dannonba...@me.com'.
-Dannon
On Apr 20, 2011, at 12:42 PM, David Matthews wrote:
> Hi,
>
> I've followed this thread with interest. I have had a problem on one of my
> workflows, it fails
Done, many thanks...
Best Wishes,
David.
__
Dr David A. Matthews
Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.
Tel. +44 117 3312058
Fax.
Hello all. I am re-exploring Galaxy after a year hiatus. While I searched
the archives to no avail it is possible that my question/complaint was already
answered. If so, please ignore.
I find the placement of Mouse-ear Cress (arabidopsis) in the 'select a
reference genome' list to be s
Hi Peter,
Another option would be to pad out the files so that all desired columns
in the final result are present before you do the join with "Column
Join". For now, this and the method you describe are the available choices.
If you wanted to open an issue in bitbucket, the team would have a
Hello Luobin,
At this time, a restart is necessary for the dataset to be incorporated.
Thanks for using Galaxy!
Best,
Jen
Galaxy team
On 4/12/11 1:50 PM, Luobin Yang wrote:
Hi all,
I am wondering if it's possible to to reload a ".loc" file without
restarting the Galaxy server?
Thanks,
Luob
Hello Sam,
When running Megablast, filtering by identity or evalue can help reduce
the hits (the default values are all fairly permissive, if you are
performing the query vs the same species target genome and the query has
been filtered for base calling quality). Filtering out low-complexity
Hello Giovanni,
Galaxy does not (yet) support genome downloads, but a recommended source
(it was ours) would be the UCSC Genome browser. Here is a link to their
downloads ftp site. Instructions are in the README files within the file
directories. Be sure to use FTP (direct unix or a client suc
Hello Rick,
Welcome back :)
Thanks for the suggestions! Making it easier for users to locate data is
important. I'll pass these on to our genome database guru (Kelly) for
consideration.
Best wishes and let us know if you need help or have other
observations/suggestions. All feedback is appr
Hello -
Few more links that may be helpful:
http://bitbucket.org/galaxy/galaxy-central/wiki/DataTables
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies
Thanks!
Jen
On 4/20/11 1:49 PM, Jennifer Jackson wrote:
Hello Giovanni,
Galaxy does not (yet) support genome downloads, b
Dear Ann and Jeremy:
We have this discussion long time ago, and I am sorry that I brought it
up here
again. I am just thinking that as Ann said, can we add this tool which convert
bam into wig file into galaxy? Or make a workflow to generate a wig
file from a
bam file generate by tophat? In th
Hello again,
Apologies for the multiple emails, but to be clear: in Galaxy, Tophat
uses the same indexes as Bowtie (i.e. use the Bowtie instructions to get
set up).
Please let us know if we can help again,
Jen
On 4/20/11 2:14 PM, Jennifer Jackson wrote:
Hello -
Few more links that may be
On standard UNIX, the SIGHUP signal (kill -HUP ) is used to perform
this kind of actions (re-read config files) on almost all daemons [1].
Doing a quick grep:
$ grep -ri "HUP" galaxy-central
Nothing shows up, so as Jen indicated, does not seem to be implemented
at first glance... but one could h
I am not sure about IGB but IGV can take directly Bam files from Tophat
output, so should not be an issue of visualization.
Vasu
--- On Wed, 4/20/11, Ying Zhang wrote:
From: Ying Zhang
Subject: Re: [galaxy-user] get wig file after tophat
To: "Jeremy Goecks"
Cc: "Baxter, Adam" , "galaxy-u..
Thank you for the reminder and the encouraging words!
We just released IGB 6.5 (many improvements!) and are planning what to do
next.
Top on the list is to do a better job of supporting Galaxy users by making
it possible to view your "BAM" files in IGB without having to download them
first.
I w
Vasu,
Here are the steps to create this visualization; this is relatively new
functionality, and you'll want to use our test server (
http://test.g2.bx.psu.edu/ ) for now.
(1) Create a new visualization from the main menu: Visualization --> New Track
Browser and choose your genome build.
(2) A
I have to say that's a very nice visualization. Well done.
Jim
On Apr 20, 2011, at 9:28 PM, Jeremy Goecks wrote:
Vasu,
Here are the steps to create this visualization; this is relatively
new functionality, and you'll want to use our test server ( http://test.g2.bx.psu.edu/
) for now.
Hi Ying,
You're in luck because I've been working with genome browsers lately, so I
think I can help you address your problem. What you're looking for is a
visualization of a coverage histogram for the BAM reads produced by Tophat,
yes?
It turns out that some genome browsers provide this auto
I can answer IGV questions, sadly I'm still coming up to speed on
Galaxy.
I've lost track of the original question, but IGV computes a coverage
histogram on the fly, a bit like the Galaxy Track Browser, but you
have to be zoomed in. However, you can also precompute a coverage
histo
Hi everyone,
I'd like to know if i can receive digested mail only. Thanks
Sincerely,
John
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep al
27 matches
Mail list logo
