[galaxy-dev] Variable multiple output files not appearing in history

2011-12-05 Thread graham etherington (TSL)
Hi, I'm developing a barcode splitter, which will split barcodes of variable length and then put them into the history for downstream analysis (currently FASTX barcode splitter only splits barcodes of the same length and the user has to download the data through an html link). The number of output

Re: [galaxy-dev] Variable multiple output files not appearing in history

2011-12-05 Thread Dannon Baker
Graham, How are the output files being handled in split_var_length_barcodes_wrapper.py? See http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files for a reference-- you're going to want to follow the bottom example there involving $__new_file_path__ and the naming convention

Re: [galaxy-dev] Variable multiple output files not appearing in history

2011-12-05 Thread Geert Werk
Hi Graham, I've created something similar myself. I've not put it on the toolshed yet, as I have to test it further, but it seems to work as expected. See code in attachment. Best regards, geert vandeweyer University of Antwerp On 12/05/2011 12:47 PM, graham etherington (TSL) wrote: Hi,

[galaxy-dev] Urgent help needed

2011-12-05 Thread Toqa Manasrah
Hi Everybody, I am running a tool which is not defining the output file name as parameter. the tool is running and I can see the output file in the history directory but not in the history frame. how could I solve the problem? I should see and download the output file from the history but I see

Re: [galaxy-dev] Urgent help needed

2011-12-05 Thread Dannon Baker
Toqa, Just to make sure I've understood your question: the problem is that a tool that you're trying to wrap doesn't provide a way to specify a particular output filename? Take a look at the from_work_dir attribute of a data element. Or are you asking how to define outputs in general? For

Re: [galaxy-dev] possibly weird config requests...

2011-12-05 Thread Nate Coraor
On Dec 4, 2011, at 5:39 PM, Ross wrote: Hi Russell, Just addressing AD/LDAP authentication - authentication is trivially and best (IMHO) left to an external (eg apache) proxy - save yourself a lot of effort - it's known to work well. Lock down the paste process so it only talks to your

Re: [galaxy-dev] GATK / R local install configuration

2011-12-05 Thread Daniel Blankenberg
Hi Carlos, Are you using a version of GATK that is 1.3? Another possibility is that you are missing an R library (e.g. 'ggplot2'), that is used by the VariantRecalibrator for building the plots. Start up an interactive R session and type: library('ggplot2') If you are missing the library,

Re: [galaxy-dev] DB schema upgrade problem (79 - 85)

2011-12-05 Thread Nate Coraor
On Dec 5, 2011, at 3:02 PM, Leon Mei wrote: Dear all, Today I upgraded our NBIC server from an older release (fetched on July 5th, 2011) to the latest version in galaxy-dist. After execute hg update and sh manage_db upgrade and merge some local configurations, I successfully restarted

Re: [galaxy-dev] DB schema upgrade problem (79 - 85)

2011-12-05 Thread Leon Mei
Hi Nate, Here's the output of the migration: == galaxy@galaxy2:~/prog/galaxy-2011-12-5$ sh manage_db.sh upgrade 79 - 80... Migration script to create tables for disk quotas. done 80 - 81... Migration script to add a 'tool_version' column to the hda/ldda tables. done 81 - 82... Migration

Re: [galaxy-dev] Urgent help needed

2011-12-05 Thread Toqa Manasrah
Thank you so much Dannon. I appreciate your help but I need some more clarification. in the tool I am integrating (which is java classes) if the input parameters are ./main.bash eps0.3_40reads.fa population10_ref.fa 15 6 120 Then teh output is in eps0.3_40reads_I_6_15_CNTGS_DIST0_EM20.txt As

[galaxy-dev] Display VCF in IGV problem

2011-12-05 Thread Lance Parsons
I am unable to get VCF files to display in IGV in my local galaxy installation. BAM files display fine, however, whenever I click on the link to display a VCF file I get the following error message: You must import this dataset into your current history before you can view it at the

Re: [galaxy-dev] [galaxy-bugs] Problem with indexing a genome through tophat on a local copy of Galaxy...

2011-12-05 Thread Jeremy Goecks
Hi David, There should be additional information in the galaxy database about why the job failed; take a look at stderr column of the failed job using some SQL like this: -- select * from job where state='error' and tool_id='tophat' and stderr like '%indexing reference%' order by id desc; --

Re: [galaxy-dev] possibly weird config requests...

2011-12-05 Thread Smithies, Russell
Thanx guys, that should give me heaps to go on with :-) --Russell -Original Message- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Tuesday, 6 December 2011 8:21 a.m. To: Ross Cc: Smithies, Russell; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] possibly weird config

[galaxy-dev] Workflow API (runtime modification of tool parameters)

2011-12-05 Thread Richard Park
Hello, I was wondering what would be the best way to extend Galaxy's API functionality to allow for runtime modification of tool parameters? I have successfully been able to run workflows programmatically using the API, following the basic steps in: scripts/api/execute_workflow.py.

Re: [galaxy-dev] Workflow API (runtime modification of tool parameters)

2011-12-05 Thread Dannon Baker
Richard, You're correct in that currently the workflow API affords no method for runtime modification of tool parameters, other than inputs. Depending on your needs, it might be feasible to have a few static workflows that you reuse often via the workflow API. If that isn't the case, and you