I integrated Bismark in Galaxy in my server. I downloaded Bismark from
Galaxy Tool shed. I just copied the Bismark into /tools directory and added
some codes in tool_conf.xml to make it visible. Do I need to install the
real Bismark application in the server too? I am really confused here.
Thanks
_
Thanks. Helped me!
On Thu, Oct 18, 2012 at 11:02 AM, Enis Afgan wrote:
> With a certain version of Python there's been an issue stopping Galaxy
> using ctrl+C. You can use 'sh run.sh --daemon' to have the process run in
> the background and then 'sh run.sh --stop-damemon' to stop it.
>
> Hope th
With a certain version of Python there's been an issue stopping Galaxy
using ctrl+C. You can use 'sh run.sh --daemon' to have the process run in
the background and then 'sh run.sh --stop-damemon' to stop it.
Hope this helps,
Enis
On Thu, Oct 18, 2012 at 4:12 PM, Sachit Adhikari <
sachit.techner..
Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local
machine, I need to close the terminal and restart the terminal again.
However, in server I integrated several tools, now I need to restart the
server to test it. I used ./run.sh --reload doesn't restart the server and
I can't
Dave,
There's likely something problematic about your history that causing problems.
Can you share with me the history that's generating the error? To do so, from
the history options menu --> Share/Publish --> Share with a User --> my email
address
Thanks,
J.
On Oct 17, 2012, at 6:58 PM, Jen
Hi Dave,
Yes, if your Galaxy instance is on the internet, for entire history
transfer, you can skip the curl download and just enter the URL from the
public Main Galaxy server into your Galaxy directly.
To load large data over 2G that is local (datasets, not history
archives), you can use th
Hello,
Yes, this has not changed. The reference GTF given to Cuffdiff must
contain all of the transcripts of the inputs:
http://user.list.galaxyproject.org/cuffcompare-inputs-td4654384.html
Run this as you have done previously:
http://user.list.galaxyproject.org/cuffcompare-outputs-missing-td4
Hi Dave,
To export larger files, you can use a different method. Open up a
terminal window on your computer and type in at the prompt ($):
$ curl -0 '' > name_the_output
Where can be obtained by right-clicking on the disc icon for
the dataset and selecting "Copy link location".
If you are
Hi list,
Is there a currently a known problem with the "export to file" function?
I'm trying to migrate some data from the public galaxy to a private one;
the export function worked well with a small (~100mb) dataset, but it has
not been working with larger datasets (>2GB) and I get the error: Ser
Hello,
Thank you for sharing your history. The difference in FPKM values can be
explained by the use of the -N option ("Perform quartile normalization:
Yes"). Set this to "No" to avoid the variable per-run normalization.
This has also been discussed at seqanswers.com:
http://seqanswers.com/fo
Hello,
This tool is hosted on the Cistrome Analysis Pipeline (a custom Galaxy
public server). It would be best to contact them about the tool to be
certain that you receive the most current information. Their support
email (from the login page) is: cistrome-b...@jimmy.harvard.edu.
http://wik
Hello Jerzy,
The MACS wrapper in Galaxy currently supports version 1.3, which
explains the problems with 1.4. Tool dependencies are noted on this wiki:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
For the other errors, are you trying to run MACS on the command line or
within Gala
Hello Amit,
Are you using the public Main Galaxy instance at
http://main.g2.bx.psu.edu (usegalaxy.org) or another server specific to
your project?
If you are working with a project's Galaxy server, then you will need to
contact the administrator running that instance. It sounds as if you are
Hi,
I was using the tool 'Screen Motif' to find a particular motif in given region
of genome. I don't know what dose the last column in the output file stand
for. My guess is that it's -10*log(p), is it?
--
朱云依 Yunyi Zhu
中国科学技术大学University of Science a
On Tue, Oct 16, 2012 at 8:22 PM, Fang,Xiefan wrote:
> Dear Galaxy users,
>
> Does anyone know how to merge several FASTQ groomer files by using
> Galaxy? If not, is there any other program that can achieve this? The size
> of one FASTQ groomer file is around 1GB. Thank you!
>
The Galaxy
Dear Galaxy users,
Does anyone know how to merge several FASTQ groomer files by using
Galaxy? If not, is there any other program that can achieve this? The size of
one FASTQ groomer file is around 1GB. Thank you!
Best regards,
Xiefan Fang, Ph.D.
Postdoctoral associate
Department of Pe
Hello,
I cannot run MACS on the local Galaxy. When I install MACS version 1.4.,
it gives error something like "cannot find macs". When I install version
1.3.7.1 it gives error "/line 34, in from MACS.OptValidator
import opt_validate ImportError: No module named MACS.OptValidator"/
I sourced
Does anyone knows a step-by-step pipeline to SNP calling on illumina
dataset?
>From the alignment to the end
thanks
Francesco
--
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the publ
Hi,
I am a first time user in galaxy for analysis of my RNA-Seq data.
I am facing problem in loading data in galaxy.
1.I successfully transfered fastq files (from Illumina) by FTP and then
tried to upload by checking each files and execute.
3. Initially it was yellow (with rotating c
Hello forum,
I was reading some of the theory behind cuffdiff and how it calculates
for DE genes.
My question:
if I do not have replicates, how does cuffdiff do the test statistic
which is dependent on the variance?
The manual says "Note that in order to calculate the test statistic T,
we need to
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