Dear users,
Could anybody suggest the valid DESeq toolshed for RNA sequencing???
Thanks
Sridhar
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Hi Sridhar,
we are developing a DESeq2 tool at the moment, if you want to join get
in touch with me. Its developed here:
https://github.com/bgruening/galaxytools/tree/master/deseq2
I will upload our latest progress during the day.
Cheers,
Bjoern
Dear users,
Could anybody suggest the
Sure ..
Thanks for the reply..
On Tue, Aug 20, 2013 at 12:33 PM, Bjoern Gruening bjoern.gruen...@gmail.com
wrote:
Hi Sridhar,
we are developing a DESeq2 tool at the moment, if you want to join get
in touch with me. Its developed here:
On Tue, Aug 20, 2013 at 2:57 PM, John Chilton chil...@msi.umn.edu wrote:
I don't have time to argue about this especially because I agree that
cc is likely better than OSS licenses, but I am just too passionate
about this point not too. Workflows are 100% software!!!
I think we agree here -
Hello,
I'm trying to add a new data source to my Galaxy instance, using
synchronous data depositing.
The data source needs to know the email address of the user who tries to
import data to the Galaxy server. I would have like to write something
like that:
inputs
Hello Bjoern,
This issue should be resolved in change set 10412:29ab5a6d75a7, whcih is
currently running on both tool sheds. No changes should be necessary to any of
your current dependency definition files.
This changeset was committed to the stable branch, so production Galaxy
environments
I solved my problem using dynamic_options. Thank you
Date: Mon, 19 Aug 2013 09:14:28 +0200
From: h...@fmi.ch
To: ramao_tiago_tibur...@hotmail.com
CC: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Getting data from a database to create a dynamic
combo box
Hi Ramon
You need to
I have a tool that uses two dates to fetch data in a database.
I am using a parameter type called datetime in the field type. It uses
javascript and allows a date to be selected through a calendar. When I use it
as a tool works perfectly, but when I try to use the workflow got an error.
When I
Hello all,
At one of the GCC2013 Birds of a Feather
sessionshttp://wiki.galaxyproject.org/Events/GCC2013/BoF/PublicGalaxyServers
the
group was very clear that they would like to see less frequent releases of
Galaxy. We're currently aiming to do a release every 2 months and have
been pretty
Hello Bjoern,
I believe this issue was corrected in changeset 10412:29ab5a6d75a7, which was
committed to the stable branch and is running on both tool sheds. At least I
am unable to reproduce the behavior you describe using 3 similar repositories
in my local tool shed. Please let me know if
Hi Peter,
I believe this behavior is resolved with change set 10412:29ab5a6d75a7, which
was committed to the stable branch and is running on both tool sheds. You'll
need to update your Galaxy instance to get the fix. Pleaser let me know if I
have misunderstood the steps necessary to
Thanks for reporting this, Petere - we'll take a look as soon as we get a
chance.
I've created the following Trello card for this issue.
https://trello.com/c/CZeVLNFr/1068-toolshed-bullet-points-not-displayed-in-repository-readme-files
Greg Von Kuster
On Aug 20, 2013, at 6:56 AM, Peter Cock
Hello,
I'm working on a project to integrate a Galaxy instance with a remote
software execution service. The service maintains a catalogue of
applications, storage and execution hosts, files (input and output) and
jobs (submitted, executing, finished, etc) all manageable through REST
Peter and Ross,
I've not been able to reproduce this behavior, most likely because I am not
following the precise steps you've used when you see it. Can you clarify what
you do when you encounter it?
Thanks!
Greg Von Kuster
On Aug 15, 2013, at 4:50 AM, Peter Cock p.j.a.c...@googlemail.com
Hi everyone,
Is there a way to set the name of the file which is downloaded by the user?
The output name is, for example, Results.zip, but when I download the file,
the name cames as Galaxy-100[Results.zip].data. I would like to receive the
file with the name Results.zip. Is it possible?
Best
Hi,
I guess you're downloading a results file form the history. If so, when Galaxy prompts to you save as you can choose any name you like. It works for me.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
OK, I've solved it. The issue with display_as location remains and I still
have to put the Allow from directives in the / location but I have been able to
get UCSC working again and I'm completely to blame so maybe I should keep quiet
but no, in the spirit of sharing one's idiocy here it is
Just to close this e-mail thread out, blend4j is now available in the
maven central repository. You can add it to your maven project with
the following dependency definition:
dependency
groupIdcom.github.jmchilton.blend4j/groupId
artifactIdblend4j/artifactId
Hi All,
Thanks for the suggestions. I installed the Toolshed ( Differential_Count
(version 0.21) ). It asks for the input matrix - rows are contigs, columns
are counts for each sample.
Any idea on how to generate this matrix file??
Thanks
On Tue, Aug 20, 2013 at 12:53 PM, Mahtab Mirmomeni
Sridhar,
If you read the tool form help text for the differential count tool, you
will have noticed that right at the top, it says:
Requires a count matrix as a tabular file. These are best made using the
companion HTSeq based counter Galaxy wrapper and your fave gene model to
generate
You can use htseq_bams_to_count_matrix repository by fubar in the test
toolshed.
On Wed, Aug 21, 2013 at 2:37 PM, Sridhar Srinivasan
sridhar2bioi...@gmail.com wrote:
Hi All,
Thanks for the suggestions. I installed the Toolshed ( Differential_Count
(version 0.21) ). It asks for the input
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