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.edu>>
Date: Wednesday, 12 February 2014 13:44
To: "graham etherington (TSL)"
mailto:graham.ethering...@sainsbury-laboratory.ac.uk>>,
Galaxy Dev mailto:galaxy-dev@lists.bx.psu.edu>>
Subject: Re: [galaxy-dev] Error installing VarScan from Toolshed
Graham,
I'v
Hi,
I’m trying to install VarScan from the Main Toolshed. I’ve tried both the
versions available (‘varscan’ from fcaramia and ‘varscan_version_2’ from
devteam), but I get the same error each time:
File
"/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install
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 a
:chil...@msi.umn.edu>>
Date: Thursday, 6 February 2014 16:54
To: "graham etherington (TSL)"
mailto:graham.ethering...@sainsbury-laboratory.ac.uk>>
Cc: Galaxy Dev mailto:galaxy-dev@lists.bx.psu.edu>>
Subject: Re: [galaxy-dev] Running Import History from File as local job
thing wrong with the xml that an error would be
thrown, so I’m not sure if there’s something else that I’m missing.
Many thanks,
Graham
From: John Chilton mailto:chil...@msi.umn.edu>>
Date: Thursday, 6 February 2014 14:32
To: "graham etherington (TSL)"
mailto:graham.etherin
Hi,
I have two local instances of Galaxy running (both entirely independent of each
other and running on separate clusters). I’m trying to export a history from
Instance A to Instance B, but so far have not been able.
I’ve attempted this in two ways.
1. Download the Galaxy_history.tar.gz file fr
Hi,
I've been getting some errors on our local Galaxy instance which haven't
been solved by updating to the latest code.
Some of them involve sql-type errors. My sys-admin informed me that "There
are a couple of SQL errors being reported, i.e. text attempting to be
inserted into an integer field wi
>
>When installed from the tool shed, data managers use the
>shed_tool_data_table_conf.xml file, could you check the contents of that
>file?
>
>Also can you check the paster.log during server start up for any errors,
>its most likely the case that this changeset
>https:
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 comman
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'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 O
on?
Cheers,
Graham
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601
On 07/02/2013 13:39, "Nate Coraor" wrote:
>On Feb 7, 2013, at 6:04 AM, graham etherington (TSL) wrote:
>
>&
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 item
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 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 mea
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,
No
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: 263
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 'b
file_path__ and the naming convention specified.
>
>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:
>
>&g
Hi,
I'm developing a barcode splitter, which will split barcodes of variable
length and then put them into the history for downstream analysis
(currently FASTX barcode splitter only splits barcodes of the same length
and the user has to download the data through an html link). The number of
output
Toqa,
In answer to your first question - you can use the "bash" interpreter as
follows:
shell_script.sh arg1 arg2 ... argN
I'll leave your second question to someone more qualified than me.
Cheers,
Graham
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwi
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 and
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