Hi,
Another way I found is to select the main frame in the galaxy window, do show
only this frame in your browser and then do a forced refresh (crtl+F5), You
can then go back to your normal galaxy window and the main frame will be
refreshed.
David
From: o...@hpc.ufl.edu
Date: Tue, 18
Hi again,
In fact, much easier way (at least if you are using Firefox). Right click in
the main frame this frame reload frame. No need to restart galaxy.
David
From: o...@hpc.ufl.edu
Date: Tue, 18 Dec 2012 12:57:56 -0500
To: margeem...@gmail.com
CC: galaxy-dev@lists.bx.psu.edu
Subject:
And when I tried running tophat alone like this:
tophat -r 20 test_ref reads_1.fq reads_2.fq
I get this error:
[2012-12-19 06:57:07] Beginning TopHat run (v2.0.7)
---
[2012-12-19 06:57:07] Checking for Bowtie
Bowtie version: 2.0.2.0
[2012-12-19
I have a bacterial genome from ncbi and woulld like to extract seq from the
corresponding fasta file of bacterial genome. Since i have list of
coordinates so would not be possible to extract one by one. Is there any
interface within galxy that i can use.
Thanks
Hi Greg,
At the very top of this wiki:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
is a link to a related wiki:
http://wiki.galaxyproject.org/Admin/Data%20Integration
that has additional required set-up info. This page also includes
information about how to rsync the indexes
Hi Everyone,
Is there a way to directly copy files from galaxy with the proper file
name? I'm currently using the galaxy API to download files via HTTP, but it
is very slow and would like to speed up the process of copying files
directly, but am having a hard time getting the proper file names.
file_name: /galaxy-central/database/files/000/dataset_733.dat
This is the dataset location on the filesystem (perhaps relative . If you
script is running on a machine that has access to the filesystem, you should be
able to simply copy it.
Best,
Jen,
I have also shared history with you File 27 and 32 are fetching empty seq
file. I think since bacterial genome is not having any Chr that may be the
problem, I tried all option just coordinates; Chr1 however the out put is
empty.
Thanks
Kanwar
On Wed, Dec 19, 2012 at 10:07 AM, Jennifer
Hello,
The format is incorrect for the interval file - the chromosome field
(c1, or the first field) should be the same as the identifier (the
line) in the fasta file. In your case, this is:
AF148805
Change what you have assigned as Chr1 to be AF148805 to make the
correction.
Take care,
It seems like tophat2 does not support --transcriptome-mismatches option
but Galaxy is still configured to call tophat2 with this option when run
with Full parameter setting option within Galaxy. Is there new wrapper
with this fix? If not, how to remove this option from Galaxy so that
tophat2 is
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