Dear galaxy users,
I tried to follow the instruction to see how the workflow worked by using the
one on the support site
Galaxy-Workflow-mt_analysis_0.01_strand-specific_(fastq_double).ga
However, it takes very very long time and remains the following state for
several hours. Is this normal? I
Hi Camilla,
For small genomes like these, the quickest option is to use the 'custom
reference genome' function with tools. Details about how to use are in
our wiki:
http://wiki.galaxyproject.org/Support#Custom_reference_genome
Hopefully this helps!
Best,
Jen
Galaxy team
On 12/18/12 12:40 P
On Dec 19, 2012, at 11:09 AM, "Sun, Wenping [USA]" wrote:
> I also have the preconfigured cloud instance set up recently. However, when I
> stopped the instances (master and cluster nodes) from aws, I couldn't get the
> galaxy web running again (the instance running however the DNS not able to
Hi Dannon,
Yes, you are correct! I installed galaxy from scratch on the cloud. I will
check the site you provided and see how it goes.
I also have the preconfigured cloud instance set up recently. However, when I
stopped the instances (master and cluster nodes) from aws, I couldn't get the
gal
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 06:
This is the error I am getting while running Tophat. What's causing this? I
have the default hg19 index files.
Error in tophat:
[Tue Dec 18 10:08:33 2012] Beginning TopHat run (v1.3.3)
---
[Tue Dec 18 10:08:33 2012] Preparing output location ./tophat_ou
Kathryn,
Are you using the galaxy cloud configuration provided by the team, or have you
installed your own galaxy on a cloud instance?
It sounds like the latter, in which case you'll need to configure reference as
detailed here: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. You
may
Dear mailing list,
I am new to Galaxy and am going through the tutorials, starting with Galaxy 101.
Under point 2.5. "Recovering exon info and displaying data in genome browsers"
in the tutorial, there is the option to display data at UCSC. However, I don't
have this option, although my history lo
Dear Galaxy members,
I am new to galaxy and just installed galaxy on aws cloud. I am testing how it
works and have the following question below:
1. I tried to test bowtie2 with the dataset I uploaded, however, the
window for reference genome is very narrow and nothing from pull-down menu
Heia,
Would it be possible to add the genome of Kosmotoga olearia
(NC_012785) and Mesotoga prima (NC_017934) to the genomes availabe in
galaxy database?
Thanks,
Camilla
--
Camilla L. Nesbø
University of Alberta
Biological Sciences
116 street and 85 Avenue
Edmonton, Alberta
T6G2R3
+1 780 604 3080
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