[galaxy-dev] Problem uploading files to RNA-Rocket

Hi, I was trying to upload some FASTQ files via FTP using the FileZilla client but although the program connects to the server it doesn't log in. I checked the user and the password several times and I tried to use another account but I still got the same error. I also tried to upload the files vi

Re: [galaxy-dev] Problem uploading files to RNA-Rocket

Hey David, I'm not sure why you'd be having this issue, but I'd contact the RNA-Rocket server staff (pathporth...@vbi.vt.edu) for more assistance; this is not a Galaxy server that the Galaxy Team manages. -Dannon On Thu, Aug 21, 2014 at 9:51 AM, David Salcines wrote: > Hi, I was trying to upl

[galaxy-dev] How to build an application that uses a set of files?

Hello, I would like to get advice how to implement the following application into Galaxy: We have a set of say, 17 tabular files, we would like to present them to the User and allow him to select a subset of them, say 9. Once he selected these files we would like to invoke our program “merge.

Re: [galaxy-dev] How to build an application that uses a set of files?

Are these 17 files fairly dynamic - i.e. are they going to depend on previous steps in a history or user uploads - or are they literally just 17 more or less fixed files associated with that tool and every user should see roughly the same 17 options. -John On Thu, Aug 21, 2014 at 3:03 PM, George

Re: [galaxy-dev] How to build an application that uses a set of files?

They are totally dynamic. Say all the files of tabular type that the User has at the moment. On Thu, Aug 21, 2014 at 12:28 PM, John Chilton wrote: > Are these 17 files fairly dynamic - i.e. are they going to depend on > previous steps in a history or user uploads - or are they literally > just

Re: [galaxy-dev] How to build an application that uses a set of files?

Hmm... in that case I think you can just create a multiple input data parameter. You can iterate through the files in your tag and pass them to your merge.py file: merge.py #for $input in $inputs# $input #end for# ... This works unless you literally need 9 files - this input type doesn't sup

[galaxy-dev] Database integrity error when installing new tools from toolshed

Hi, I updated a local Galaxy installation a while back and I followed the steps listed on one of the wiki pages. The update included changes to the database schema and I was careful to backup and restore it according to the directions. However, when I try to install new tools from the tool shed or

[galaxy-dev] bioblend run_workflow (no_wait?)

I'm using bioblend to launch a workflow, but i find that the gi.workflows.run_workflow() command does not provide an option for no_wait. Can anyone provide justification for why this needs to be synchronous? -Evan Bollig Research Associate | Application Developer | User Support Consultant Minneso

Re: [galaxy-dev] bioblend run_workflow (no_wait?)

There is no reason workflow invocation *has* to be synchronous, but that's how galaxy works right now as, mostly, a historical artifact. Workflow scheduling happens inside the web request, and other than bioblend issuing the request in another thread there won't be an implementation w/ no_wait. T

Re: [galaxy-dev] bioblend run_workflow (no_wait?)

Thanks Dannon. Looking forward to the resolution. We've got some long workflows (100+ steps) that take days to compute. It takes about 2 minutes to finish queuing tasks, and then I found that they continue to execute even if I interrupt the bioblend thread. I'll add a signal.alarm interrupt to kill

Re: [galaxy-dev] bioblend run_workflow (no_wait?)

So, see the commentary on the bioblend issue you added as well, but in short -- while you should currently expect to wait while the entire workflow was queued, bioblend *should not* be blocking waiting for all jobs to complete and that sounds like a bioblend bug if it is. That's what the 'wait' pa

[galaxy-dev] Problems downloading files via bioblend

I have a python script that I use to download the qc data generated in one of the steps in a workflow. It used to work on a previous install of galaxy - but we've gone through and updated our Galaxy install so that it's now running on a new file system - and when I try and use the bioblend api t

Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY

Mira doesn’t work on Galaxy. This is the log message I receive. Tool: Assemble with MIRA v3.4 Name: MIRA log Created:Fri Aug 22 00:24:38 2014 (UTC) Filesize: 0 bytes Dbkey: ? Format: txt Galaxy Tool Version:0.0.10 Tool Version: None Tool Standard Output: stdout