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
be able to add 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
you can use label="${input.name}"
Shaun
Quoting Nikhil Joshi on Thu, 25 Aug 2011 03:10:21 -0700:
Hi Kanwei,
I tried that and it didn't seem to work. It seems like Galaxy parses the
output name BEFORE execution... although that doesn't make sense. In any
case, I couldn't get it to work.
I meant to say label="${input}" or label="${input.value}.
If it's a select field then you can change the option values to the
text you want to add to your output label.
Shaun
Quoting Kanwei Li on Wed, 24 Aug 2011 20:34:57 -0400:
Hi Nikhil,
The tool templates are Cheetah templates, s
Hi.
I am interested in putting quotas in to effect on our local Galaxy
server. From the admin page I can create a quota but this only seems
to apply to disk space. I noticed on your test site you have quotas
for concurrent jobs also. Have I missed how to set this or is this
functionality
mysql database.
Would postgres help? I am yet to see a reliable way of converting
between mysql and postgres so haven't done this yet.
Thanks
Shaun Webb
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC0
Hi. I am using the tag:
path to tool --version
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 do?
I have tried using als
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 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 nu
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
--
) MIME-Version: 1.0 Content-Type:
text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit
Generated-By: Babel 0.9.4
Any ideas where this is coming from?
Thanks
Shaun Webb
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336
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?
Tha
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
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
tly to histories? I'm not sure 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
Sco
than that Trackster has been a very valuable tool.
Thanks
Shaun Webb
Error - : [Errno 24] Too many open files:
'/storage/home/galaxy/galaxy_dist/database/files/068/dataset_68559.dat'
URL:
http://bifx-core.bio.ed.ac.uk:8080/tracks/converted_datasets_state?hda_ldda=hda&dataset_id=608c
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
t
ted 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
istry.load_datatypes( 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
Sco
' object has no attribute 'load_datatypes'
Thanks
Shaun Webb
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
- End forwarded message -
--
The University of Edinburgh is a charitable body, registered in
Sco
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
al tracks again I get new menu options (filters, tool,
tool parameter space visualisation). None of these seem to work and
trackster often stops working after doing this.
Thanks for all the effort put in to these great new features. I hope
this lengthy email is helpful!
Shaun Webb
Edi
oting Dave Bouvier on Tue, 31 Jul 2012 10:21:07 -0400:
Hello Shaun,
On 7/31/12 09:37:23.000, SHAUN WEBB wrote:
Genome indexing:
1. I realise this is just a beta feature and it will be great when fully
integrated. I tried to generate bowtie2 indexes for an installed build.
I can see the job a
Hi Greg, thanks for the response
Quoting Greg Von Kuster 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/suggestions/bug
ository
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 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 are abl
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 SC0053
refox.
Thanks
Shaun Webb
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage you
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
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 i
creating a new workflow.
Thanks
Shaun Webb
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
___
Please keep all replies on the list by using "reply all"
in your m
there is no directory dataset_85192_files. I have blast
installed and I'm able to run makeblastdb on the command line.
Do I have to make any other modifications before I can use Blast tools?
Thanks for your help
Shaun Webb
University of Edinburgh
--
The University of Edinburgh is a chari
if I can
figure it out. I'll let you kno if I find something.
Shaun
Quoting Peter Cock on Wed, 5 Dec 2012
15:44:47 +:
On Wed, Dec 5, 2012 at 2:37 PM, Shaun Webb wrote:
I have just installed the Blast+ tools from the Galaxy tool shed and tried
to make a Blast DB from a fasta
where can I find them?
Thanks
Shaun Webb
Error - : u'ensembl_Current'
URL:
http://bifx-core.bio.ed.ac.uk:8080/galaxy/display_application/4100358d24a8f6e2/ensembl_interval/ensembl_Current
File
'/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/p
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
-
lease send a link 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 hav
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
em 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 numbe
Hi, I am creating a tutorial using galaxy pages and I want to add a
contents section at the top to link to headings further down the page.
I can't quite figure out how to use the anchoring.
Thanks for your help.
Shaun Webb
--
The University of Edinburgh is a charitable body, regis
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.
1. Non-admin users with add permissions on a library are offered the
option to upload from file systems path. Should this be restricted to
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
Scot
on is removed.
Shaun
Quoting Greg Von Kuster :
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.
1. Non-
ld be great.
Thanks.
Shaun Webb
paste.httpserver.ThreadPool INFO 2011-03-09 09:49:49,962 No idle
tasks, and only 0 busy tasks; adding 5 more workers
paste.httpserver.ThreadPool INFO 2011-03-09 09:49:58,754 No idle
tasks, and only 4 busy tasks; adding 1 more workers
paste.httpserver.ThreadPool
Hi, I really like the new feature to show dataset information and
parameters used to run the tool. Problem is that the link doesn't
always work. It seems as though the first time I open a history and
click the "i" the information is displayed in the main screen, but
after that none of the
2011 10:15:13 +
From: SHAUN WEBB
Subject: Galaxy process
To: galaxy dev
Hi,
since making the last update I have found some new warnings in my
paster.log, it also seems as though the galaxy process starts to
gather memory and eventually hang (35% of 64G memory).
I've
ent
repo.
Thanks Shaun,
Greg Von Kuster
On Mar 10, 2011, at 5:21 AM, SHAUN WEBB wrote:
Further to my email below.
I have a data library that contains many ~117Gb of NGS data,
uploaded via file system path. This library was always slow to open
(about 10s) but now takes several minutes or
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 Univer
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 d
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 mult
Hi,
I am creating a tool that provides the user with different input
options based on the format of the input file. I have a conditional
statement:
Type1
Type2
Type3
etc.
There is overlap between the options available for each file t
Hi Galaxy team,
I created a new repository on the tool shed called "test", I wanted to
see what steps were required to publish a tool before I go ahead and
release the production version. I then tried to change the name of the
repository and got a server error.
When I search for test, tr
ntation on what is required to publish a new tool
in the tool shed?
Shaun
Quoting Greg Von Kuster 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 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?
Are you eventually
Hi,
I am trying to write a tool xml file and want to do the following:
I have a number of GTF files stored locally and referenced in a data
table. I give the user a drop down list of those available using the
following code:
I then want them to choose an annotation type based on
"Selecting no tables will result in using all tables."
from_file="annotation_profiler_options.xml"/>
and here is an example from the microbial import tool:
On Jul 13, 2011, at 6:17 AM, SHAUN WEBB wrote:
Hi
;Values from selected gtf file" />
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 file each
time.
In this case I want the first select to choose which
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
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, in
from ga
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
"/storage/home/galaxy/te
Ignore previous email, I found the error, it was not a Galaxy problem
Thanks
Shaun
Quoting SHAUN WEBB 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, it doesn't
hat makes sense.
Thanks
Shaun
Quoting SHAUN WEBB on Fri, 15 Jul 2011
10:17:44 +0100:
Hi Greg,
thanks for the suggestion. This line doesn't seem to work:
Galaxy looks for a file at galaxy_dir/tool-data/some_value rather
than the value given in the .loc file
I would also like t
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