[galaxy-dev] Import error : no module named ...

Hi all, Happy new year! I have western mysteries that I cannot resolve. I have a local instance of galaxy and while this instance run correctly since several hours or days, suddenly the jobs fail and this error appears : Import error : no module named CistromeAP.jianlib.inout CistromeAP is the n

Re: [galaxy-dev] Very confused about workflow_step_connection table?

output_step_id and input_step_id are both foreign keys to the workflow step table. For example, the first row defines a connection between the output named "output" of workflow_step id=1 to the input named "input_file" of the workflow_step with id=2. The input and output names come from the tool a

Re: [galaxy-dev] What is the difference between the table stored_workflow and workflow in Galaxy?

This pattern is used to implement versioning. Every time a workflow is saved a new entry in the "workflow" table is created. The "stored_workflow" table keeps a pointer ("latest_workflow_id") to the most recent. ___ Please keep all replies on

Re: [galaxy-dev] File import recovery

On Dec 31, 2012, at 8:18 PM, Kyle Ellrott wrote: > I'm currently adding a large number of files into my Galaxy instance's > dataset library. During the import some of the files (a small percentage) > failed with: > > /inside/depot4/galaxy/set_metadata.sh: line 4: 14790 Segmentation fault

Re: [galaxy-dev] MGTAXA taxonomic prediction does not work...

I assume you are using the mgtaxa Galaxy instance at JCVI. I've copied the mgtaxa maintainer on this message. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Dec 28, 2012 at 11:56 AM, Edlund, Anna wrote: > Hello. > > > > My name is Anna Edlund and I have loaded severa

Re: [galaxy-dev] Very confused about workflow_step_connection table?

Ok. So they are the foreign key from which table? Or the same table workflow_step_connection? On Wed, Jan 2, 2013 at 9:04 PM, James Taylor wrote: > output_step_id and input_step_id are both foreign keys to the workflow > step table. > > For example, the first row defines a connection between the

Re: [galaxy-dev] Very confused about workflow_step_connection table?

To the "workflow_step" table. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, Jan 2, 2013 at 10:48 AM, Sachit Adhikari wrote: > Ok. So they are the foreign key from which table? Or the same table > workflow_step_connection? > > > On Wed, Jan 2, 2013 at 9:04 PM, James

Re: [galaxy-dev] Very confused about workflow_step_connection table?

Oh Alright. Thanks James! On Wed, Jan 2, 2013 at 9:34 PM, James Taylor wrote: > To the "workflow_step" table. > > -- > James Taylor, Assistant Professor, Biology/CS, Emory University > > > On Wed, Jan 2, 2013 at 10:48 AM, Sachit Adhikari > wrote: > > Ok. So they are the foreign key from which t

[galaxy-dev] Error downloading files from Galaxy

Dear Galaxy Developers, My user name is henry...@petermac.org I'm having issues downloading files (which is an issue I didn't used to have), particularly ones which have >50 columns. These can be uploaded, but then cannot be downloaded from the server. I have attached an example txt file an

Re: [galaxy-dev] Error downloading files from Galaxy

Thanks for catching this. You are correct in that it only affects files which have > 50 columns. I'll have a fix for this in shortly. -Dannon On Jan 2, 2013, at 8:28 AM, To Henry wrote: > > Dear Galaxy Developers, > > My user name is henry...@petermac.org > > I'm having issues downloadi

[galaxy-dev] January 2013 Galaxy Update

Hello all, The January 2013 Galaxy Update is now available. *Highlights:* - New papers - Open Positions

[galaxy-dev] Repository not found after pull

Hi list, I installed the Homer tool from the main toolshed. Then I uninstalled it and made a pull for the new galaxy revision. When I tried to re-install Homer I got a HTTP:NOT FOUND error... My guess is that the url for the original Homer is stored in the DB (and it got changed on the new revisi

Re: [galaxy-dev] Repository not found after pull

Hi Franco, We are not able to reproduce this behavior in any of our test/development instances. The repository clone url is not stored in the database, but only the information necessary to provide the various features available for managing an installed tool shed repository in Galaxy. If you

Re: [galaxy-dev] Galaxy for SNP chip data

Arthur, On Mon, Dec 31, 2012 at 2:03 PM, Goldberg, Arthur P < arthur.p.goldb...@mssm.edu> wrote: > > We have SNP microarrays about hundreds of subjects. In particular, samples > were processed on the Illumina Infinium HumanExome BeadChip, with 951,117 > markers.. Our project is collaborative, so

[galaxy-dev] backtrace when attempting to view a shared workflow

File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 202 in display_by_username_and_slug return self.display(trans, stored_workflow) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 218 in display self.g

Re: [galaxy-dev] Where is the output of tools stored in Galaxy?

Hi, I guess to preserve both you could write a little bit of python that created a link in the folder you would like to send the output to. This would mean galaxy would be tracking the new file and you would have a file in a folder of your choice. Cheers James. On Fri, Dec 28, 2012 at 12:18 AM,