[galaxy-dev] reasonable linux box specs

2013-11-15 Thread Andrew Norman
Hi all I'd like to set up a local installation of Galaxy on a dedicated linux machine. I've taken a look at the Galaxy appliance, but since I'm the only one in my lab who will be using it, it's outside my price range. I'm going to be doing RNA seq read mapping and differential expression

Re: [galaxy-dev] Converting .gff3 to 12-column .bed

2013-11-15 Thread Lindsay Rutter
Hello Jennifer: Thank you so much for the descriptions, and for sharing the method to check that the difference in line count is appropriate. Sincerely, Lindsay Rutter On Tue, Nov 12, 2013 at 7:09 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Lindsay, Nice to hear that Vipin's server

[galaxy-dev] LDAP user auth

2013-11-15 Thread Jon Ambler
Good morning! I am setting up a galaxy instance at our department and I was hoping to use our LDAP database to authenticate users to use galaxy, So my questions are: How would one tell galaxy to refer to the LDAP database? Would this allow new users to be automatically created on first login?

Re: [galaxy-dev] LDAP user auth

2013-11-15 Thread Rasche Eric
Morning Jon, See this page: http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy Under 'mod_authnz_ldap' you'll find relevant information (assuming you're using mod_authnz_ldap) Users will be created on first login, which means you'll have to have them login and then assign groups (as far as

[galaxy-dev] Empty tool panel

2013-11-15 Thread Yec'han Laizet
Hi, In the current version of galaxy stable branch (5c789ab4144a), the tool panel is empty when installed (freshly and out of the box) on my production server (ubuntu server 12.04). If I copy this galaxy folder onto my laptop, the tool panel shows up (ubuntu 13.10). Do you have an idea of

Re: [galaxy-dev] Galaxy wrappers for CLC Assembly Cell (CLCbio)

2013-11-15 Thread Peter Cock
On Wed, Oct 30, 2013 at 4:03 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hello all, This is just to announce I am working on a wrapper for CLC Assembly Cell which is the CLCbio commercial command line assembly tool suite. http://www.clcbio.com/products/clc-assembly-cell/ Our institute

Re: [galaxy-dev] Failed to generate job destination

2013-11-15 Thread John Chilton
It looks like you have tools with no matching id in toolbox.tools_by_id. Given the complexity of your job_conf.xml I assume you are using multiple Galaxy processes? Have you installed stuff from the tool shed or migrated tools and not restarted all Galaxy processes, or did you try to restart

Re: [galaxy-dev] Galaxy environment on local resources

2013-11-15 Thread John Chilton
I am responding to galaxy-dev because others may have better answers than me. On Wed, Nov 13, 2013 at 9:38 PM, Alistair Chilcott alistair.chilc...@utas.edu.au wrote: John, Thanks for the advice, a dose of realism is always useful. :D I suspect that our current installation is fiddly

Re: [galaxy-dev] Setting a queue for torque submission

2013-11-15 Thread Nate Coraor
Xian and I were able to resolve this on IRC, the problem is is that no default queue is specified in the PBS client (intentionally) and the `-q` param was improperly handled in the pbs job runner (it expected param id=“destination” instead). This has been fixed in the stable branch in

[galaxy-dev] how to add openstack in biocloudcentral ?

2013-11-15 Thread Jennifer Jackson
Hello Zeeshan, Let's post this over to the proper list, galaxy-...@bx.psu.edu, and see if that helps. You could also contact Brad, the git repository owner, directly about questions that involve biocloud. Best, Jen Galaxy team http://wiki.galaxyproject.org/MailingLists#The_lists On 11/15/13

Re: [galaxy-dev] reasonable linux box specs

2013-11-15 Thread Jeremy Goecks
Without details about your incoming data rate and size, it's very difficult to answer this question. I suggest taking some of your data, running it on our public server (usegalaxy.org), and seeing how long it takes. RNA-seq tools (Tophat, Cufflinks, etc.) use 4 cores for a job, so you can

Re: [galaxy-dev] Empty tool panel

2013-11-15 Thread Jeremy Goecks
Do you see any errors in the JavaScript console? Does this only happen on particular Web browsers? J. On Nov 15, 2013, at 10:15 AM, Yec'han Laizet ylai...@pierroton.inra.fr wrote: Hi, In the current version of galaxy stable branch (5c789ab4144a), the tool panel is empty when installed