Hi,
is there any current functionality or plans to enforce secure
passwords when registering a new account? By secure I mean tests on
length, use of capitals and alphanumeric characters etc.
Thanks
Shaun Webb
--
The University of Edinburgh is a charitable body, registered in
Scotland
Hi,
I was just wondering if anyone has put any work in to developing
wrappers for casOT:
http://eendb.zfgenetics.org/casot/index.php
Couldn't see anything in the toolshed. If not I'll have a go myself.
Shaun Webb
--
The University of Edinburgh is a charitable body, registered in
Scotland
is with the tool.
The error is rather vague, can anyone point me to what could possibly
cause this error?
Thanks
Shaun Webb
University of Edinburgh
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336
is happening here and
what is failing?
Thanks
Shaun Webb
University of Edinburgh
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
___
Please keep all replies on the list by using
and note the dataset with the problem.
Thanks,
Jen
Galaxy team
On 3/19/13 2:44 AM, Shaun Webb wrote:
Hi, I have lost my view in UCSC link on my customtrack datatypes,
I'm not sure when this happened. External display links are still
working ok for other datatypes. I have set the genome database
Hi, I have lost my view in UCSC link on my customtrack datatypes, I'm
not sure when this happened. External display links are still working
ok for other datatypes. I have set the genome database to hg18.
Any idea what I will need to edit to get this back?
Thanks
Shaun webb
if I can
figure it out. I'll let you kno if I find something.
Shaun
Quoting Peter Cock p.j.a.c...@googlemail.com on Wed, 5 Dec 2012
15:44:47 +:
On Wed, Dec 5, 2012 at 2:37 PM, Shaun Webb swe...@staffmail.ed.ac.uk wrote:
I have just installed the Blast+ tools from the Galaxy tool
creating a new workflow.
Thanks
Shaun Webb
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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I am looking at bigwig files in trackster.
When I zoom in the point where 20kb is displayed on screen I get large
blocks of the track separated by empty gaps. When I zoom in to these
gaps there is definitely track signal there. Is this a bug or is this
intended to limit the amount of data
to be cloned in the first place.
Thanks again!
Greg
On Aug 1, 2012, at 7:03 AM, SHAUN WEBB wrote:
Quoting Greg Von Kuster g...@bx.psu.edu on Wed, 1 Aug 2012 06:23:11 -0400:
I cannot reproduce this behavior, so can you let me know the steps
you use to do so? I need the page on which you
Hi all,
I would like to change the name of the directory where my Galaxy
instance is installed. What is the best way to go about this without
breaking any paths/links.
Thanks
Shaun
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number
Hi Greg, thanks for the response
Quoting Greg Von Kuster g...@bx.psu.edu on Tue, 31 Jul 2012 11:50:36 -0400:
Hi Shaun,
On Jul 31, 2012, at 9:37 AM, SHAUN WEBB wrote:
Hi, I have been trying out the latest version of Galaxy and a newly
installed local toolshed and I have a few questions
previously
http://gmod.827538.n3.nabble.com/Error-loading-data-tt4013269.html).
Thanks in advance for any help
Shaun Webb
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336
( root_dir=sys.argv[1], config=sys.argv[2] )
AttributeError: 'Registry' object has no attribute 'load_datatypes'
Thanks
Shaun Webb
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336
Hi,
is there any plan to add capability to delete multiple datasets at
once, similar to the copy datasets interface in the history options
menu.
If I am running workflows and want to delete all the created datasets
(during testing or if I've used the wrong parameters etc) it is quite
by the owner? Any tips would be good, trying to free up some
space on our server.
Thanks
Shaun Webb
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
___
Please keep all
what the best way to
implement this would be but I'd like to see an improvement.
Thanks to all the Galaxy team
Shaun Webb
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336
by looking at properly mapped paired
ends in a bam file and extending coverage across the distance between
them.
Thanks
Shaun Webb
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336
: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of SHAUN WEBB
Sent: Monday, December 12, 2011 8:40 AM
To: galaxy dev
Subject: [galaxy-dev] googlebot
Hi,
my paster.log is full of errors relating to a googlebot trying to
access a library file.
I
Hi,
my paster.log is full of errors relating to a googlebot trying to
access a library file.
I noticed a robots.txt file in the static folder configured as such.
User-agent: *
Disallow: /
I thought this would stop all bots accessing all files. Should this be
configured differently?
Hi, I updated my test server today and everything seemed fine. I added
a new library item via a URL. After that my history panel displays
Internal Server Error and I am getting the error below in paster.log:
Any ideas how this has occurred and if there is a fix?
Shaun
Hi Nate.
Could you provide more info on how to run this script. I have a
history and dataset name and I want to find the file stored on the
server.
Thanks
Shaun
Thanks Assaf,
This has come up enough times that I've just committed a script that
will return the filename if provided a
Hi. I am using the upload tool to enter some test data in the text box
and checking the convert spaces to tabs box. However Galaxy is setting
the file as txt rather than tabular, this seems to be a new bug.
Shaun
--
The University of Edinburgh is a charitable body, registered in
Scotland,
Hi. I am using the tag:
version_stringpath to tool --version/version_string
In my xml file. I would expect the tool version to be printed in the
information window for each dataset but the version field is blank. I
am running the latest Galaxy dist, is there anything else I need to
you can use label=${input.name}
Shaun
Quoting Nikhil Joshi najo...@ucdavis.edu on Thu, 25 Aug 2011 03:10:21 -0700:
Hi Kanwei,
I tried that and it didn't seem to work. It seems like Galaxy parses the
output name BEFORE execution... although that doesn't make sense. In any
case, I
read_name to the truncated output (when
not printing all fields). This makes downstream analysis a lot easier,
e.g. looking at reads that map multiple times.
Thanks
Shaun Webb
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336
=1/
/options
/param
Hope that makes sense.
Thanks
Shaun
Quoting SHAUN WEBB swe...@staffmail.ed.ac.uk on Fri, 15 Jul 2011
10:17:44 +0100:
Hi Greg,
thanks for the suggestion. This line doesn't seem to work:
options from_file=some_value
Galaxy looks for a file at galaxy_dir
Hi all,
I'm getting the following error running a custom tool. I'm not really
sure where the problem is coming from, it doesn't happen every time I
run the tool. Can anyone point me in the right direction?
Thanks
Shaun
Traceback (most recent call last):
File
Ignore previous email, I found the error, it was not a Galaxy problem
Thanks
Shaun
Quoting SHAUN WEBB swe...@staffmail.ed.ac.uk on Mon, 25 Jul 2011
11:21:43 +0100:
Hi all,
I'm getting the following error running a custom tool. I'm not
really sure where the problem is coming from
Hi, I recently update to the latest dist release and I'm getting this
error whenever I try to upload files
Traceback (most recent call last):
File
/storage/home/galaxy/test/galaxy-dist/tools/data_source/upload.py,
line 11, in
from galaxy.datatypes.checkers import *
ImportError:
, 2011 at 11:31 AM, SHAUN WEBB
swe...@staffmail.ed.ac.uk wrote:
Hi, I recently update to the latest dist release and I'm getting this error
whenever I try to upload files
Traceback (most recent call last):
File /storage/home/galaxy/test/galaxy-dist/tools/data_source/upload.py,
line 11
=name index=2/
column name=some_value index=1/
/options
/when
/conditional
On Jul 13, 2011, at 9:45 AM, SHAUN WEBB wrote:
Hi Greg, I'm not sure if this answers my question. Using
options_from_file is fine if I want to refer to the same
on what is required to publish a new tool
in the tool shed?
Shaun
Quoting Greg Von Kuster g...@bx.psu.edu on Tue, 12 Jul 2011 10:24:28 -0400:
Hello Shaun,
On Jul 12, 2011, at 6:07 AM, SHAUN WEBB wrote:
Hi Galaxy team,
I created a new repository on the tool shed called test, I wanted
I am, but I would like to be able to change the category. It will be
an RNA-seq tool.
Shaun
Quoting Greg Von Kuster g...@bx.psu.edu on Tue, 12 Jul 2011 12:38:08 -0400:
On Jul 12, 2011, at 11:54 AM, SHAUN WEBB wrote:
Thanks Greg, could you delete the repository I created please
Hi, I have created a tool that will fetch sequences for selected IDs
from a tabular file containing multiple IDs and additional info.
I want the tool config to scan the first column of the tab file for
IDs and provide the user with a selection box where they can select a
single ID or
Hi,
I have a tool that takes a zipped archive as input, finds all the
sequence files (~90 of them), separates them by barcode, does a little
extra processing and outputs a single fasta file. I would like this to
run on Galaxy in a workflow with a few other tools.
I know there have been
We are experiencing issues with workflows where jobs are running
before the previous step is completed (especially with large
workflows). I am wondering if the problem is MySQL.
Does anyone know of a reliable script for converting a MySQL dump to
PostgreSQL?
Thanks
Shaun
--
The
is removed.
Shaun
Quoting Greg Von Kuster g...@bx.psu.edu:
Hello Shaun,
Thanks for your message.
On Feb 11, 2011, at 6:54 AM, SHAUN WEBB wrote:
Hi, I have notice a few problems which may or may not have been
fixed in the latest distribution (I am yet to update) but wanted to
make you aware
I seem to remember there being talk of a parameter you can set in the
universe file that allows you to limit the size of files for which
metadata is set when galaxy uploads a file.
Was this put in to production?
Shaun
--
The University of Edinburgh is a charitable body, registered in
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