[galaxy-dev] Links to anchors in Pages

2011-02-01 Thread SHAUN WEBB
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, registered

[galaxy-dev] Setting Metadata

2011-02-11 Thread SHAUN WEBB
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

Re: [galaxy-dev] Data Library Upload Issues

2011-02-15 Thread SHAUN WEBB
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

[galaxy-dev] Galaxy process

2011-03-09 Thread SHAUN WEBB
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 INFO

[galaxy-dev] Info button

2011-03-09 Thread SHAUN WEBB
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

[galaxy-dev] Fwd: Galaxy process

2011-03-10 Thread SHAUN WEBB
10:15:13 + From: SHAUN WEBB swe...@staffmail.ed.ac.uk Subject: Galaxy process To: galaxy dev galaxy-...@bx.psu.edu 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

Re: [galaxy-dev] Fwd: Galaxy process

2011-03-10 Thread SHAUN WEBB
development 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

[galaxy-dev] MySQL 2 Postgres

2011-03-30 Thread SHAUN WEBB
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

[galaxy-dev] Uploading Zip Files

2011-05-03 Thread SHAUN WEBB
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

[galaxy-dev] options from file

2011-05-06 Thread SHAUN WEBB
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

[galaxy-dev] Tool Shed Problem

2011-07-12 Thread SHAUN WEBB
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, try

Re: [galaxy-dev] Tool Shed Problem

2011-07-12 Thread SHAUN WEBB
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

Re: [galaxy-dev] Tool Shed Problem

2011-07-12 Thread SHAUN WEBB
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

Re: [galaxy-dev] Tool XML parameter options from locally stored files

2011-07-15 Thread SHAUN WEBB
=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

[galaxy-dev] checkers

2011-07-18 Thread SHAUN WEBB
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:

Re: [galaxy-dev] checkers

2011-07-18 Thread SHAUN WEBB
, 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

[galaxy-dev] Error preparing job

2011-07-25 Thread SHAUN WEBB
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

Re: [galaxy-dev] Error preparing job - PLEASE IGNORE PREVIOUS

2011-07-25 Thread SHAUN WEBB
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

Re: [galaxy-dev] Tool XML parameter options from locally stored files

2011-07-27 Thread SHAUN WEBB
=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

[galaxy-dev] Sam2interval.py bug

2011-08-02 Thread SHAUN WEBB
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

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-08-25 Thread SHAUN WEBB
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

[galaxy-dev] Version String

2011-10-13 Thread SHAUN WEBB
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

[galaxy-dev] Tab sniffer

2011-10-14 Thread SHAUN WEBB
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,

Re: [galaxy-dev] HOW TO RETRIEVE DATA FROM HISTORY??!!

2011-10-20 Thread SHAUN WEBB
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

[galaxy-dev] Server Error after Update

2011-10-27 Thread SHAUN WEBB
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

[galaxy-dev] googlebot

2011-12-12 Thread SHAUN WEBB
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?

Re: [galaxy-dev] googlebot

2011-12-13 Thread SHAUN WEBB
: 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

[galaxy-dev] Coverage for paired end data

2012-02-01 Thread SHAUN WEBB
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] Feature requests - viewing data and annotations

2012-02-03 Thread SHAUN WEBB
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

[galaxy-dev] Delete multiple datasets

2012-04-24 Thread SHAUN WEBB
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

[galaxy-dev] Deleted datasets

2012-04-24 Thread SHAUN WEBB
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

[galaxy-dev] Error loading data

2012-05-16 Thread SHAUN WEBB
( 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

[galaxy-dev] Problem with proxy

2012-06-21 Thread SHAUN WEBB
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

Re: [galaxy-dev] Galaxy and Toolshed issues

2012-08-01 Thread SHAUN WEBB
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

Re: [galaxy-dev] Galaxy and Toolshed issues

2012-08-08 Thread SHAUN WEBB
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

[galaxy-dev] Changing Install Directory

2012-08-08 Thread SHAUN WEBB
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

[galaxy-dev] Trackster Bug

2012-08-15 Thread SHAUN WEBB
. 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 your subscriptions

[galaxy-dev] Another trackster issue?

2012-08-15 Thread SHAUN WEBB
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

[galaxy-dev] Workflow loading problem

2012-11-30 Thread Shaun Webb
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 mail client

Re: [galaxy-dev] Blast+ tools

2012-12-05 Thread 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

[galaxy-dev] customtrack visualisation

2013-03-19 Thread Shaun Webb
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

Re: [galaxy-dev] customtrack visualisation

2013-03-20 Thread Shaun Webb
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

[galaxy-dev] Manage Local data

2013-03-26 Thread Shaun Webb
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

[galaxy-dev] Tool shed tool error

2013-06-07 Thread Shaun Webb
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

[galaxy-dev] casOT wrapper

2014-01-21 Thread Shaun Webb
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

[galaxy-dev] Secure Passwords

2014-07-30 Thread Shaun Webb
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