ove the overall quality is to do the experiment again.
> And why is there a difference between the mean and median in the fastqc
> report at each cycle?
>
It means your quality score distribution is skewed. This is not necessarily
a concern.
--
James Taylor, Associate P
Galaxy's FTP support uses ProFTPD, which has modules for both TLS
(FTPS) and SFTP.
--
James Taylor, Associate Professor, Biology/CS, Emory University
On Tue, Sep 24, 2013 at 7:58 AM, Georgios Magklaras
wrote:
> Hi,
>
> Our team at the University of Oslo is building a Life
should then be able to dump and load easily
enough, you will just need to move the dump file between servers.
--
James Taylor, Associate Professor, Biology/CS, Emory University
On Mon, Sep 23, 2013 at 3:36 PM, Lei Yan wrote:
> Dear Dannon,
>
> I built a new cloud Galaxy instance today
distribution are here:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jun 11, 2013 at 9:20 AM, Elwood Linney wrote:
> Hello, I will try this again without attachments and hope it gets on the
> list.
>
> I want to add Ray (a scalable de novo assembler for genomes and metagenomes)
> to Galaxy.
And I really want you to do this!
> I will also have to write a wrapper for Ray to prepare the command line from
> the options provided by the
> Galaxy API.
>
>
> But where is stored the executable (in my
Sarah, when you share with a specfic user, it will not show up under
the "Shared Data" section since that is only for published items. The
person you share it with should see it under "Histories Shared with
me" which is in the History options menu:
--
James Taylor, Assistant P
Hi, could you be more specific. Name one or two specific tools that
are not working. Also, when does the error occur, after submitting the
job or before loading the tool?
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, May 24, 2013 at 10:31 AM, Eduardo Fox wrote
Are the first four lines of your file deliberately whitespace? This
will definitely cause problems for file type detection (it is not a
valid TSV file as is).
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Sun, May 12, 2013 at 10:52 AM, Chunyu Liu wrote:
> hi,
> I
Since you have isolated the problem to running on ceph, I'm not sure
there is much help we can offer. My understanding is that the posix
filesystem part of ceph (as opposed to the object store) is still in
development and could have bugs.
--
James Taylor, Assistant Professor, Biology/CS,
Hi, it appears the nexus file you are trying to visualize does not
have any "trees" section, what does the newick format tree look like,
and did these work before in Galaxy? If you could share the relevant
history that would help.
--
James Taylor, Assistant Professor, Biology/CS, Emory
Hi Michael, sorry it took a while but we've figured out the root cause
of this issue and will be deploying a fix shortly. Thanks!
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Mar 22, 2013 at 4:20 PM, Michael Axtell wrote:
> Hi everyone.
>
> I
Yes, you will need to edit universe_wsgi.ini and change the entry for "host
=" (exactly what you need to do is documented in that file).
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, Mar 13, 2013 at 3:40 AM, Michael Milevskiy wrote:
>
You are definitely in uncharted territory with an arm server. Can you
try building just bx-python itself and let us know what the errors
are?
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, Feb 21, 2013 at 11:03 AM, Shun Liang wrote:
> Hi,
>
> I am trying t
Okay. In Galaxy, what genome build (dbkey) is selected for the dataset?
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Feb 1, 2013 at 3:09 PM, Kilaru, Varun wrote:
> Hi Professor James Taylor,
>
> Good day. Its a .wig file I downloaded from GEO. I tried
What is the type of the file from GEO? Any additional information you
provide will help debug this.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Feb 1, 2013 at 1:53 PM, Kilaru, Varun wrote:
> Hi,
> Good day. I have been trying to use trackster on a
looking for.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jan 15, 2013 at 8:52 PM, wrote:
> Hi
>
>Sorry if these questions are obvious but I just don’t know how to find
> the answers.
>
>
>
> I’m trying to get one of the API ex
You are probably seeing the mtDNA re-sequencing datasets associated
with this paper:
http://genomebiology.com/2011/12/6/R59
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Jan 4, 2013 at 10:46 AM, Sun, Wenping [USA] wrote:
> Hello,
>
>
>
> It is go
You probably need to sudo to sgeadmin (cloudman guys correct me if you
have this setup differently).
I don't see any reason not to make worker nodes submit hosts by
default in a future cloudman release.
-- jt
On Thu, Sep 13, 2012 at 4:17 PM, greg wrote:
> As a follow up I found a command that
Roberta, I'm traveling right now so I'm forwarding your message to our
help list. Thanks.
-- Forwarded message --
From: Roberta Galletti
Date: Tue, Sep 11, 2012 at 5:19 AM
Subject: Re: Galaxy: RNA-seq analysis problems
To: James Taylor
Hello James,
sorry to bother
Lali, we don't have an answer yet because we have never seen this and can't
reproduce. Are you using a proxy server or anything unusual?
-- jt
(composed on my phone)
On Apr 6, 2011, at 9:49 AM, Lali wrote:
> Btw Anton, you never answered anything about the bug with the history not
> loading
Excerpts from Sonali Amonkar's message of Sun Jan 16 17:17:14 + 2011:
> I agree what you mentioned on Tools. Does Galaxy have any provision
> for executing Workflows from command line too?
Currently I don't think this is implemented, but the plan is that this
would be done through the API.
>
ing at some point. We'll try to take another look at this
soon. No workaround unfortunately.
--
James Taylor, Assistant Professor, Biology / Computer Science, Emory University
___
galaxy-user mailing list
galaxy-user@lists.bx.psu.edu
http://lists.bx.p
n the MAF block
> retrieve from Galaxy).
Can you point out an example of this? In particular, are you sure you
are using the same original alignments in Galaxy and the Genome Browser?
Thanks,
James
--
James Taylor, Assistant Professor, Biology /
Two parts to this probably.
1) It should definitely be possible to have parameters in tool configs
that are set in a global configuration file, I actually thought
tool_conf.xml might be a good place (inside the tool element).
2) For the particular case of processor cores, ideally we would b
24 matches
Mail list logo
