Dear UK Galaxy-devs,
We're delighted to announce the launch of the UK Galaxy Community.
Please visit the site and have a look around:
http://galaxy-community.org.uk/
The aims of Galaxy-UK are:
* To bring the Galaxy community in the United Kingdom closer together
* Identify and address
...@bx.psu.edumailto:d...@bx.psu.edu
Date: Wednesday, 12 February 2014 13:44
To: graham etherington (TSL)
graham.ethering...@sainsbury-laboratory.ac.ukmailto:graham.ethering...@sainsbury-laboratory.ac.uk,
Galaxy Dev galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Error
Hi Philippe,
I’m unable to suggest a reason as to why this has happened, other than some
sort of corruption whilst the job was running, but I would point out two things
to you.
1. I don’t think you need to run the fastq groomer on your data anyway as it’s
in Illumina 1.8+ format, which should
I’m not sure if there’s something else that I’m missing.
Many thanks,
Graham
From: John Chilton chil...@msi.umn.edumailto:chil...@msi.umn.edu
Date: Thursday, 6 February 2014 14:32
To: graham etherington (TSL)
graham.ethering...@sainsbury-laboratory.ac.ukmailto:graham.ethering...@sainsbury
...@msi.umn.edumailto:chil...@msi.umn.edu
Date: Thursday, 6 February 2014 16:54
To: graham etherington (TSL)
graham.ethering...@sainsbury-laboratory.ac.ukmailto:graham.ethering...@sainsbury-laboratory.ac.uk
Cc: Galaxy Dev galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev
in
the main file.
Thanks for using Galaxy,
Dan
On Jul 12, 2013, at 8:14 AM, graham etherington (TSL) wrote:
Hi,
I've tried using the Data Manager (Admin Data Manage local data
(beta)) to install builds for BWA and Samtools on my local Galaxy
instance.
Previous to using the Data Manager, I
Sridha,
There's a difference between your two errors. In the first error for
fastqc, Galaxy can't find the source.
In the second error, for GATK, the source is being found and executed OK,
but GATK is throwing an error (The fasta file you specified
(/tmp/tmp-gatk-EYMIaT) does not exist.). I'm not
Hi,
I've tried using the Data Manager (Admin Data Manage local data
(beta)) to install builds for BWA and Samtools on my local Galaxy instance.
Previous to using the Data Manager, I used to add the build to
tool-data/shared/ucsc/builds.txt, create the .fai indexes (for samtools)
from the command
Hi,
I'm trying to see if I can style Galaxy tools, so instead of all the input
fields being a long list one after the other, I can align a few of the
fields side-by-side.
Has anyone any suggestions on how I might accomplish this?
Best wishes,
Graham
Dr. Graham Etherington
Bioinformatics Support
Hi,
Some of our users are experiencing problems with (mainly) tabular data on
our local install of Galaxy (changeset 8368:0042b30216fc, Nov 06 2012).
I'm presuming it's some kind of meta-data problem.
The first strange behavior is that they are getting green history items,
but when the history
Hi Suzan,
The problem here is that there's an absence of data for one of the genes
you want to compare, so one can't really assign any significance to that
particular gene or transcript.
This would require inventing a singificance value where if a gene is
highly expressed in one sample, but not
Hi Nikhil,
Purging datasets is covered in the Galaxy Wiki.
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Purge%20Histories%20and%
20Datasets
Basically, there's a bunch of scripts in
{GALAXY_HOME}/scripts/cleanup_datasets/ that require running.
We've created a single .sh file that executes
Hi,
The Galaxy Toolshed is giving a 502 Bad Gateway error. Is there a problem
with it at the moment?
If so, is it just a matter of restarting it or is there a likelihood of it
being down for a while?
Cheers,
Graham
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Hi Nate,
We are getting quite large discrepancies between 'Size on disk' and
'Usage' numbers, so I've run the scripts/set_user_disk_usage.py script.
When I run it, some of the 'old usage' numbers are negative numbers, e.g.
User1 old usage: -226417886261, new usage: 139894688577
User2 old usage:
Hi,
I've created a java app tested it from the command line and put it in the
shared/jars folder. It runs for a while and then the history item turns
red. If I view the dataset output though, everything is as should be, i.e.
the expected output from the tool is seen.
If I click on the view error
.
On a side note, this is something I've brushed up against recently
myself, I'd be very interested in seeing what you come up with.
-Dannon
On Dec 5, 2011, at 6:47 AM, graham etherington (TSL) wrote:
Hi,
I'm developing a barcode splitter, which will split barcodes of variable
length
Hi,
I have a tool where the user selects their datasets from a drop-down list.
The drop down list obviously contains the names of the suitable datasets
as shown in the history and not that which is stored in the Galaxy
database (e.g. ../database/files/011/dataset_11377.dat)
I'm trying to access
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