Dear Galaxy user,
As Galaxy usage is growing exponentially, it has become necessary to
overhaul our development and support processes. Part of this overhaul
means defining the purpose of our mailing lists a bit better.
This list, galaxy-user (see URL  below), should be used for any
general questions and discussion regarding Galaxy usage, especially
pertaining to the public sites hosted by the Galaxy Team. We'll also
use it for announcements relevant to the Galaxy user community.
A separate list, galaxy-dev (see URL  below), should be used for
discussion and questions regarding local installations and development
of Galaxy. There is a growing "universe" of people running their own
galaxies or developing tools. This list is for them.
As before, galaxy-bugs(a)bx.psu.edu should be used for reporting specific
problems with our public sites.
The take-home message
galaxy-user = questions about Galaxy's public sites (e.g., "How do I
plot distribution base qualities?")
galaxy-dev = questions about code base, installation, and tool
technicalities (e.g., "How do I set Galaxy to talk to a cluster running
PBS or SGE?")
galaxy-bugs = any problem should be reported here (e.g., "WTF, Galaxy is
As always, thanks for using Galaxy!
Apache LDAP pass through authentication works fine for us as is with
the security branch. I haven't tried it with the current trunk. The
Galaxy roles/groups interface is being managed by our IRB admin - very
easy and attractive option - but of course, independent and out of
sync with our ldap groups.
Mind you, in some ways the separation is convenient...in other ways
it's inconsistent and redundant - but not a showstopper for us as we
currently only have about 30 users (out of 1000+ in the LDAP tree!)
who have IRB approvals to manage.
The problem of using LDAP to manage groups and have Galaxy use those
is that AFAIK there are no decent tools a non-tech savy administrator
can use to administer an LDAP tree - we've written our own based on an
LDAP adapter I wrote for Zope a long time ago, but LDAP really is a
bit of a pain for non technical administrators and we don't want our
system administrator wasting time with it if we can avoid that! So,
I'm not even sure I'd swap away from the currently redundant but very
convenient_to_manage situation, even if/when Galaxy can retrieve
groups from an LDAP server.
On Thu, Apr 2, 2009 at 3:00 AM, <galaxy-user-request(a)bx.psu.edu> wrote:
> Message: 4
> Date: Wed, 01 Apr 2009 10:48:15 -0400
> From: Nate Coraor <nate(a)bx.psu.edu>
> Subject: Re: [galaxy-user] Is Galaxy LDAP-aware?
> To: erant(a)psb.vib-ugent.be
> Cc: galaxy <galaxy-user(a)bx.psu.edu>
> Message-ID: <49D37EAF.2060907(a)bx.psu.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Erick Antezana wrote:
>> is it possible to use LDAP authentication in the Galaxy framework? If
>> not, any plans to consider it?
> Hi Erick,
> Authentication can be delegated to an upstream proxy server (e.g.
> Apache). Instructions for this are in our wiki:
> There are plans for Galaxy to at least support LDAP for user and group
> management, but this has not yet been implemented.
Ross Lazarus, Associate Professor, DACP, Harvard Medical School.
Director of Bioinformatics, Channing Laboratory, BWH
181 Longwood Ave., Boston MA 02115, USA.
I'm wondering if galaxy understands the UCSC data points format (for
example, the one produced by exporting phastcons17way scores. All I
managed to do so far is import these data into galaxy, but I couldn't find
any supported operations for this format.
It would be very useful, for example, if galaxy could convert these data
into genomic intervals using a user-defined threshold (eg, extract regions
with phastcons scores > 0.5) - but maybe it can already do it and I just
don't know how?
Mikhail Spivakov, PhD
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD
Tel +44 (0) 1223 49 26 60
Mob +44 (0) 7985 09 66 75
is there a tool or an intelligent way to add an conditional execution of
a step within a workflow? and as an extension of such tool/feature I
would be interested in just executing for instance a particular brach of
my workflow (depending on a condition from a previous step)...