Re: [galaxy-dev] Galaxy Cloudman - How to analyse 1TB data ?

Hi Enis 1. I first created the LVM on 2 new volumes. 2. Mounted the LVM 3. I stopped all services (SGE, PostgreSQL, Galaxy). 4. Copied all data on filesystem /mnt/galaxyData to the LVM 5. Umounted /mnt/galaxyData 6. Mounted LVM to /mnt/galaxyData 7.

[galaxy-dev] Illumina HiSeq 2000 external service type XML

Hi everyone, Does anyone have a typical external service type XML file for an Illumina HiSeq 2000? I have created one but not sure if its correct and there is no guide for creating the external service type XMLs thanks, Leandros ___ Please

Re: [galaxy-dev] Functional tests

Frank, I can't see anything that would cause this behavior by looking at your logs, so I cannot answer what is causing this problem in your environment. Basically it seems that nose is not finding any of the Python test scripts in the test subdirectory in your Galaxy installation directory,

Re: [galaxy-dev] Extracting the metrics files from a composite file such as Picard

Yeah...I was thinking something like that...I think it is possible to produce a varied amount of datafiles If I recall correctly...http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20FilesThonOn Feb 20, 2012, at 07:11 PM, Ross ross.laza...@gmail.com wrote:Thon, I just had an idea - write a

Re: [galaxy-dev] advanced parameters: all or nothing?

So is the behavior of the optional=true tag that if the field form is left empty for that parameter then it will not be passed to the tool? Optional is enforced at the UI level; a wrapper can choose to handle optional parameters differently. I am wondering if a more sophisticated behavior

[galaxy-dev] Error 500 when trying to execute a workflow with the API

Hi,I tried to run a workflow with the API, but get an Error 500 when I try to run the WF...The paster.log shows the following error...$ workflow_execute.py 92cc01ed93dc0f0fc91e3ded35497c0a http://srp106:8080/api/workflows ebfb8f50c6abde6d 'TEST the API'

Re: [galaxy-dev] Error 500 when trying to execute a workflow with the API

Hi, Also, if it is in fact a history id and you will be using 'hda', remember to use 'hist_id=history_id' instead of 'Test API History'. -Carlos On Tue, Feb 21, 2012 at 6:46 PM, Dannon Baker dannonba...@me.com wrote: Hi Thon, You have the right idea about what's going wrong here.  Galaxy is

Re: [galaxy-dev] Error 500 when trying to execute a workflow with the API

Hi Danon,thanks for the info...Indeed I had tried hda (I sorta figured H was for History, LD was for Library Dataset) but I got an error complaining about step 91 (I only had one step) but I figured out that the API probably uses a different number of the steps, so this worked./display.py

Re: [galaxy-dev] Error 500 when trying to execute a workflow with the API

Hi Dannon, I think he is referring to the dataset input key in the dictionary. Thon, I think this thread could be helpful: http://galaxy-development-list-archive.2308389.n4.nabble.com/Using-workflows-with-steps-with-several-inputs-through-the-API-td4267374.html In summary, you want to ./display

[galaxy-dev] strange error having to do with stderr redirection?

Hi all, I have been writing an R script to run as a tool in galaxy and it seems to work just fine. I needed to add some fine-grained error detection in the script and I wanted it to produce a red X if the error occurred. In order to do this I wrote to the stderr handle. Before I had put in the

Re: [galaxy-dev] strange error having to do with stderr redirection?

Hi, Nikhil, In my experience, R chatters to stderr in an unhelpful way such as to let you know a package got loaded or a function got masked... That's the main reason I've given up trying to execute R as a command directly - I find myself writing python wrappers (usually to call Rscript using