galaxy-user April 2009

galaxy-user@lists.galaxyproject.org

16 participants
15 discussions

Galaxy mailing list changes
by Nate Coraor 03 Apr '09

03 Apr '09

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. galaxy-user list ---------------- This list, galaxy-user (see URL [1] 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. galaxy-dev list --------------- A separate list, galaxy-dev (see URL [2] 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. galaxy-bugs list ---------------- 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 down!") As always, thanks for using Galaxy! [1] http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user [2] http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev [3] http://g2.trac.bx.psu.edu/wiki/HowToInstall --nate Galaxy Team

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Re: [galaxy-user] galaxy-user Digest, Vol 34, Issue 1
by Ross 01 Apr '09

01 Apr '09

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: > > http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy > > 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.

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does galaxy support the UCSC data points format?
by Mikhail Spivakov 01 Apr '09

01 Apr '09

Hi everyone, 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? Many thanks Mikhail -- Mikhail Spivakov, PhD Postdoctoral Fellow European Molecular Biology Laboratory Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD UK Tel +44 (0) 1223 49 26 60 Mob +44 (0) 7985 09 66 75 spivakov(a)ebi.ac.uk

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Is Galaxy LDAP-aware?
by Erick Antezana 01 Apr '09

01 Apr '09

Hi, is it possible to use LDAP authentication in the Galaxy framework? If not, any plans to consider it? thanks, Erick

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Conditional execution (workflow)
by Erick Antezana 01 Apr '09

01 Apr '09

Hello, 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)... thanks, Erick

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galaxy-user April 2009