[galaxy-dev] tool for RepeatMasker?

2011-11-27 Thread Smithies, Russell
Has anyone created a tool for running RepeatMasker http://www.repeatmasker.org/ within Galaxy? It's something we'd like to do so we can create workflows where the fasta is masked before being searched with blast. Thanx, Russell Smithies New Zealand

Re: [galaxy-dev] tool for RepeatMasker?

2011-11-27 Thread Smithies, Russell
schrieb Smithies, Russell: Has anyone created a tool for running RepeatMasker http://www.repeatmasker.org/ within Galaxy? It’s something we’d like to do so we can create workflows where the fasta is masked before being searched with blast. Thanx, Russell Smithies New

[galaxy-dev] proxy settings?

2011-11-29 Thread Smithies, Russell
I'm new to Galaxy so I'm not sure if this a Galaxy or linux/apache question . When I try to Get Data from UCSC or any other external site, I get a 407 error from our proxy as I need to authenticate. Is the request going out as the 'galaxy' user or 'apache' or the user that's logged in? I

Re: [galaxy-dev] proxy settings?

2011-11-29 Thread Smithies, Russell
Found the cure - just required adding urllib2.ProxyHandler in the data_source tools. Why doesn't Galaxy pick up the system http_proxy variables? --Russell Smithies From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Smithies, Russell Sent

Re: [galaxy-dev] proxy settings?

2011-12-04 Thread Smithies, Russell
settings but I've never managed to get that working! --Russell -Original Message- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Friday, 2 December 2011 7:03 a.m. To: Smithies, Russell Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] proxy settings? On Nov 29, 2011, at 9

[galaxy-dev] possibly weird config requests...

2011-12-04 Thread Smithies, Russell
This may be a list of weird requests but our Galaxy server runs internally and is only accessible to our users so I'd like to make it a bit easier to manage. I could customize a copy but hopefully some of the features I'm after are already available. If not, I'm happy to work on them and

Re: [galaxy-dev] possibly weird config requests...

2011-12-05 Thread Smithies, Russell
Thanx guys, that should give me heaps to go on with :-) --Russell -Original Message- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Tuesday, 6 December 2011 8:21 a.m. To: Ross Cc: Smithies, Russell; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] possibly weird config

[galaxy-dev] scripts in welcome.html?

2012-06-13 Thread Smithies, Russell
To stop users forgetting whether they're on our development or production servers I'd like to put a simple script in welcome.html to echo the hostname (or some other stuff) I've tried both javascript and php but no luck. Is this supported or should I dig further into our Apache config? Or is

Re: [galaxy-dev] scripts in welcome.html?

2012-06-13 Thread Smithies, Russell
It does of course work, just my scripting skills have faded with lack of use :( --Russell From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Smithies, Russell Sent: Thursday, 14 June 2012 10:37 a.m. To: galaxy-dev@lists.bx.psu.edu Subject

[galaxy-dev] re-writing username for login or stripping domain from remote_user?

2012-07-16 Thread Smithies, Russell
I have a situation I'm sure others have faced but I can't see how to solve it without hacking the src and I'd rather not do that just yet as it complicates upgrades. We're using Apache with NTLM and require valid user so it's a corporate domain and only authorized users are allowed access. If

[galaxy-dev] NTLM auth not passing http_remote_user?

2012-07-17 Thread Smithies, Russell
It appears that NTLM isn't passing the HTTP_REMOTE_USER through for us. Anyone else struck this and found a solution? Our apache config looks like this: Location / AuthName Galaxy NTLMAuth on NTLMAuthHelper /usr/bin/ntlm_auth --helper-protocol=squid-2.5-ntlmssp

Re: [galaxy-dev] NTLM auth not passing http_remote_user?

2012-07-17 Thread Smithies, Russell
Gordon [mailto:gor...@cshl.edu] Sent: Wednesday, 18 July 2012 9:59 a.m. To: Smithies, Russell Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] NTLM auth not passing http_remote_user? Hello Russell, Smithies, Russell wrote, On 07/17/2012 05:41 PM: It appears that NTLM isn't passing

Re: [galaxy-dev] NTLM auth not passing http_remote_user?

2012-07-17 Thread Smithies, Russell
%{LA-U:REMOTE_USER} .+\\(.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{RU}e /Location --Russell -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Smithies, Russell Sent: Wednesday, 18

[galaxy-dev] dns lookup failure and proxy errors from internal toolshed?

2012-07-22 Thread Smithies, Russell
I'm trying to setup an internal toolshed but am getting DNS and proxy errors: (I'm using port 8081 instead of 9009) The proxy server received an invalid response from an upstream server. The proxy server could not handle the request GET

Re: [galaxy-dev] dns lookup failure and proxy errors from internal toolshed?

2012-07-22 Thread Smithies, Russell
/browse_valid_repositories Was missing a trailing slash in the URL in tool_sheds_conf.xml :- ( --Russell From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Smithies, Russell Sent: Monday, 23 July 2012 3:40 p.m. To: galaxy-dev@lists.bx.psu.edu

Re: [galaxy-dev] Upload local files

2012-07-30 Thread Smithies, Russell
Yes, we'd like to do this as well. Our users data are all on the servers, not on their Windows PCs and requiring the admin create shared data libraries is an overhead we'd rather avoid. Thanx, Russell Smithies Infrastructure Technician T 03 489 9085 M 027 4734 600 E

[galaxy-dev] Custom Cheetah filters?

2013-02-12 Thread Smithies, Russell
I want to add a filter to strip whitespace and newlines from a text input box so I can pipe the sanitized string to a command. Documentation is a bit sparse (and my Python a bit basic) so does anyone have an example? Perhaps there's a better way of doing it - regex maybe? Any ideas? Thanx,

Re: [galaxy-dev] Fwd: Custom Cheetah filters?

2013-02-12 Thread Smithies, Russell
, Smithies, Russell russell.smith...@agresearch.co.nzmailto:russell.smith...@agresearch.co.nz wrote: I want to add a filter to strip whitespace and newlines from a text input box so I can pipe the sanitized string to a command. Documentation is a bit sparse (and my Python a bit basic) so does anyone have

[galaxy-dev] dynamic select problem

2013-02-20 Thread Smithies, Russell
I've been tweaking the blast+ tool xml to simplify database selection for our users (we have a lot of databases) and have made it multi-tiered through the use of two select boxen and a filter. Basically, I've added an extra column to blastdb.loc with a group name, then use this as a filter to

[galaxy-dev] Better descriptions in job history?

2014-03-31 Thread Smithies, Russell
Not sure if I've overlooked a setting somewhere, but is it possible to customize or tweak the job descriptions that are displayed in the history? Eg. Compute sequence length on data 1 isn't very descriptive, but if perhaps the annotation field or a description field could be added it would make

[galaxy-dev] Managing large database lists in tool wrappers?

2014-03-31 Thread Smithies, Russell
Does anyone have a workable solution to managing and displaying large lists in tool wrappers? eg. a database list containing hundreds of enteries in the blast+ tool? (we have 1,056 different blast databases). As a work-around we've split our blast databases into species (eg cow, sheep, fungus,

Re: [galaxy-dev] Managing large database lists in tool wrappers?

2014-03-31 Thread Smithies, Russell
like a http://ivaynberg.github.io/select2/ field work for you? What do you mean with include tags? Are you aware of Galaxy macros? https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML_Macros Cheers, Bjoern Am 31.03.2014 22:58, schrieb Smithies, Russell: Does anyone have

Re: [galaxy-dev] Managing large database lists in tool wrappers?

2014-03-31 Thread Smithies, Russell
Those macros look great and are exactly what I want :-) Thanx, --Russell -Original Message- From: Björn Grüning [mailto:bjoern.gruen...@gmail.com] Sent: Tuesday, 1 April 2014 11:07 a.m. To: Smithies, Russell; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Managing