Hello,
I performed 6 different runs of Cufflinks using the same Reference Annotation
on 6 different samples. I expected the resulting tabular output to be constant
given the same Reference Annotation was used each time. What I found is that
there was an inconsistency.
Specific example, here
Yes. For example setting "library_import_dir =
/GALAXY_PATH/database/files/import", you would do something like:
$ cd /GALAXY_PATH/database/files/import
$ ln -s /sequences/fasta/maize
$ ln -s /home/$USERNAME/blastdb_loc
After this, you will have the option of selecting from "maize" or
"blastdb_lo
Hello -
I have noticed on our local install, that the job scripts as well as
stdout/err in our cluster_files_directory is not getting cleaned up. When I
track the jobs in our runner logs, for a sampling of the job scripts left
over in the cluster_files_directory, the jobs are completing out
succes
Hi Congmao,
So others reading this know what we are talking about, this is the wiki:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
The tools listed without version numbers are those without any known
issues with either the common used current versions or standard
utilities packaged
Hello,
Do you mean a symlink ?
> From: carlos.borr...@gmail.com
> Date: Wed, 14 Mar 2012 12:57:29 -0400
> Subject: Re: [galaxy-dev] Change "Manage data Libraries"
> To: nsi...@hotmail.com
> CC: galaxy-dev@lists.bx.psu.edu
>
> On Wed, Mar 14, 2012 at 6:07 AM, Sivasangari NANDY wrote:
> > I've tr
Leandro,
For refresh_on_change to work you need a set of optional selections and a set
of refresh_on_change values, so in your example, the type should probably be a
select instead of data. You'll also need the select list options to be
generated based on your history items (at least that's wh
Hello Blanca,
Are you still have trouble determining where you disc is being used? If
so, perhaps the information in this wiki can help:
http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Delete_vs_Delete_Permanently
Please let us know if you have questions,
Best,
Jen
Galaxy team
On 3/1/1
Dear Jeremy,
On Wed, Mar 21, 2012 at 1:37 PM, Jeremy Goecks wrote:
>
> Maybe we don't understand the feature in the documentation, but this
> isn't the refresh_on_change functionality. In the Tophat tool XML
> there are no refresh_on_change="true" attributes, you are talking
> about a conditional
Dear all,
Whether it is ok to any version of some certain software if there is no version
number listed in the brackets? For example, liftOver (UCSC) (), Perl (), awk ()
and etc. Many thanks!
Best wishes,
Congmao
___
Please keep all replies
Hi Jen,
Many thanks for this, much appreciated. Will give it a try - fingers crossed!
David.
Sent from my phone, so please excuse my mistakes.
-Original Message-
From: Jennifer Jackson
Sent: 20/03/2012 18:32
To: David Matthews; Galaxy Dev
Cc: galaxy-user; Jeremy Goecks
Subject: Re: [galax
Hi Dannon,
Yes...the tags have piled up. I will apply this fix and try to remove some
of the existing tags.
Thanks for your suggestion.
Liisa
From: Dannon Baker
To: Liisa Koski
Cc: galaxy-dev@lists.bx.psu.edu
Date: 21/03/2012 09:08 AM
Subject:Re: [galaxy-dev] Can't clone
Liisa,
I'm not able to reproduce this locally with a fresh galaxy-dist. Is there
anything unique about your workflows or configuration here? And, this might be
a long shot, but do you frequently use tags with your workflows? There was an
issue that I've fixed with this recently that would ca
>
> Maybe we don't understand the feature in the documentation, but this
> isn't the refresh_on_change functionality. In the Tophat tool XML
> there are no refresh_on_change="true" attributes, you are talking
> about a conditional tag which when changing will refresh the page in
> order to expose
Dear Jeremy,
On Tue, Mar 20, 2012 at 6:19 PM, Jeremy Goecks wrote:
> Leandro,
>
> refresh_on_change is used quite a bit throughout the tool UI and appears to
> work fine both on a local instance and on the public instance. E.g. look at
> Tophat and change settings from 'Use Defaults' to 'Full P
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