Redirecting tool output doesn't make much sense because running subsequent
tools/performing downstream analyses—such as using Cufflinks to assemble Tophat
output—cannot be done in Galaxy.
I like the spirit of James' approach, though for sustained Galaxy usage, I'd
recommend symbolically linking
Hello and thank you for your reply.
I am using the online version Galaxy/MGTAXA at mgtaxa.jcvi.org
I am currently using 1.8 MB and maybe that is too much?
Thank you.
Anna
-Original Message-
From: ja...@taylorlab.org [mailto:ja...@taylorlab.org] On Behalf Of James Taylor
Sent: W
Hello, I am having a problem accessing the "custom builds" toolset. I am
getting an error message when I click on custom builds, and this has been
happening for few weeks now. Any advice you can give would be greatly
appreciated. Thanks
___
I am trying to view html results from the SeqPos Tool on Galaxy/Cistrome Main,
but keep receiving "Please use a frames compatible browser when viewing this
output" message. I have tried this in Google Chrome, IE9, and Firefox but
receive the same message in all three browsers.
_
hi,
i am trying to merge several bam files with samtools merge on the galaxy
server. i did this a few days ago with the same files successfully but when
i tried to run this merge on the same files again, i have had some strange
behavior from galaxy server. first, the commands didn't start to run f
*Hi *
*Happy New Year!*
*I hope this is the correct email to contact re. Galaxy cloud. I tried to
run Galaxy on the cloud, I could upload the file but could not go beyond
simple function "operate on genomic intervals". Is this normal? This is my
first time using the Galaxy on the cloud. Hope to h
Hello
Is it possible to redirect the GATK tools in my local installation of Galaxy to
use GATK Lite (which is free) rather than GATK. If so what files would need to
be altered and how? I'm particularly interested in getting the "Depth of
Coverage" tool to work.
Thanks much
Mark
This mes
Hi,I installed PICARD from the main tool shed in the latest update from galaxy-dist and when I clicked on the picard installed dependency link in the admin tool, I got this...Error Traceback:View as: Interactive | Text | XML (full)⇝ TypeError: 'NoneType' object is not iterableURL: http://srv1
Got this when trying CIRCSTER on latest galaxy-dist.Does this mean my system does not know about certain genomes?Trackster works fine...ThonError Traceback:View as: Interactive | Text | XML (full)⇝ TypeError: argument of type 'NoneType' is not iterableURL: http://srv151/visualization/circster
To follow up...My data file had a build key assigned to it:Tool: BAM to BigWigName:BAM to BigWig on data 31Created:Jan 04, 2013Filesize:39.9 MBDbkey:hg19-decoyFormat:bigwigTool Version:Tool Standard Output:stdoutTool Standard Error:stderrTool Exit Code:0Full Path:/mnt/ngs/analysis/svcgalaxy/DATA/fi
You could rename the file from "GenomeAnalysisTKLite.jar" to "GenomeAnalysisTK.jar" in the directory where you placed GATK...Something like/home/svcgalaxy/g/tool-data/shared/jars/gatkand it should work...ThonOn Jan 03, 2013, at 02:54 PM, mark.r...@syngenta.com wrote:Hello Is it possible to redirect
Good catch; fixed in -central changeset 8d7d70348e52
Thanks,
J.
On Jan 3, 2013, at 7:50 PM, Anthonius deBoer wrote:
> To follow up...
> My data file had a build key assigned to it:
>
> Tool: BAM to BigWig
> Name: BAM to BigWig on data 31
> Created: Jan 04, 2013
> Filesize: 39.9 MB
> Db
*Hi *
*Happy New Year!*
*I hope this is the correct email to contact re. Galaxy cloud. I tried to
run Galaxy on the cloud, I could upload the file but could not go beyond
simple function "operate on genomic intervals". Is this normal? This is my
first time using the Galaxy on the cloud. Hope to h
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