Re: [galaxy-dev] Galaxy for Natural Language Processing

2015-04-24 Thread Nicola Soranzo
Il 24.04.2015 03:18 Keith Suderman ha scritto: This can be done via the ToolShed. I assume your custom command interpreter is not different than python or perl as interpreter? One difference is that my interpreter is a Java program. I likely should have mentioned that little detail... anyone

Re: [galaxy-dev] Data Libraries

2015-04-24 Thread Nicola Soranzo
You may just use a different folder for each project inside a Sequencing library. Would that work? Nicola Il 24.04.2015 13:10 Ryan G ha scritto: This could work. In the long run though, after sequencing for a project, we'd like them people in the sequencing lab to be able to add the data to

Re: [galaxy-dev] Data Libraries

2015-04-24 Thread Ryan G
This could work. In the long run though, after sequencing for a project, we'd like them people in the sequencing lab to be able to add the data to Galaxy in project specific libraries, without having an admin create a library for them. On Thu, Apr 23, 2015 at 4:56 PM, Martin Čech

Re: [galaxy-dev] question about splitting bams

2015-04-24 Thread Roberto Alonso CIPF
Hello, I have been reading those different threads and I have some doubts that you maybe can clarify me. In the thread you said: ability to write tools that split up a single input into a collection. , I think this is focused for workflows, but in any case, could we use this to split bams?

Re: [galaxy-dev] Job submission failed

2015-04-24 Thread John Chilton
I am pretty stumped by this - my next actions would be to upgrade to the newest latest_15.03 in case this has been fixed. If that doesn't fix it I might look at your proxy configuration - is there a proxy server sitting in front of Galaxy? It looks like upload works on this server and I believe

[galaxy-dev] History panel error

2015-04-24 Thread Jose Juan Almagro Armenteros
Hello all, I have updated my Galaxy distribution today to the latest version 15.03 and the history panel is not being shown. The history seems to be there but Galaxy can't display the datasets. Even if I create a new history and I run a tool the dataset is not shown. It is just displayed an

Re: [galaxy-dev] Galaxy for Natural Language Processing

2015-04-24 Thread Bjoern Gruening
On 24.04.2015 03:18, Keith Suderman wrote: Hi Björn, On Apr 22, 2015, at 8:00 AM, Björn Grüning bjoern.gruen...@gmail.com mailto:bjoern.gruen...@gmail.com wrote: Do you have a beer preference? Outing: I'm one of the rare Germans that do not drink alcohol ;) That must be awkward ;) :)

[galaxy-dev] SSL/LDAP configuration for CloudMan/Galaxy

2015-04-24 Thread David Kovalic
Hi, We are interested in running CloudMan/Galaxy with SSL and LDAP. After searching around on the internet it seems like this is achievable and probably not too difficult, but there is no current complete “cookbook recipe” for doing so, so I thought it best to ask questions before I go ahead and

Re: [galaxy-dev] History panel error

2015-04-24 Thread Dannon Baker
Hi Jose, Can you review (and share, maybe) the relevant part of the logs from when you attempt to execute a job? It'd be worth it, if you still have the logs, to know what the Internal Server Error indicated in your first message was, as well. -Dannon On Fri, Apr 24, 2015 at 11:00 AM Jose Juan

Re: [galaxy-dev] InvalidRequestError: kombu.transport.sqlalchemy.Queue

2015-04-24 Thread Dannon Baker
Hi Asma, This is a known issue I'm still working on a permanent fix for. For right now, you can simply restart the process and it'll hopefully work fine -- we'll have a much better fix out soon. -Dannon On Thu, Apr 23, 2015 at 2:12 PM Asma Riyaz asmariya...@gmail.com wrote: Hi, I am

Re: [galaxy-dev] History panel error

2015-04-24 Thread Jose Juan Almagro Armenteros
Hi again, Now it is working, I just went back to the previous version and updated it again. All is okay except that the job table in the postgresql database is empty and is not being updated with new jobs (the problem is only with this table). I run manage_db.sh upgrade but nothing happened. Do

[galaxy-dev] README.rst missing on Tool Shed display?

2015-04-24 Thread Peter Cock
Hi all, I don't see tool README files on the main view of a repository any more. Is this a recent regression? e.g. https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools and https://testtoolshed.g2.bx.psu.edu/view/bgruening/deeptools should show the readme.rst file e.g.

[galaxy-dev] error in Galaxy (lefse)

2015-04-24 Thread Borruso Luigimaria
Dear Galaxy-project staff, in the last two weeks, I have tried several time to use Lefse but it seems to have some problem. I always get the following message: Internal Server Error Galaxy was unable to successfully complete your request. An error occurred. This may be an intermittent problem