Hi John,

I will try what we have against master.  I just went through my old emails and 
it looks like the developer branch was recommended in response to a UI issue I 
experienced with large dataset collections and not the collections themselves.  
For reference, the UI issue occurred when I inadvertently created 4K history 
items and jQuery kept timing out trying to update all the checkboxes being 
created.

The "Text file busy" error occurred on my developer machine (OS X 10.9.5, 
Python 2.7.9) with no job runner, cluster manager, or NFS.  I will run more 
tests and file proper bug reports for both issues if I can still recreate them.

Cheers
Keith

On Aug 19, 2015, at 9:48 AM, John Chilton <jmchil...@gmail.com> wrote:

> On Fri, Aug 7, 2015 at 8:01 PM, Keith Suderman <suder...@cs.vassar.edu> wrote:
>> Greetings,
>> 
>> I started pulling Galaxy code from the dev branch a few months ago to take 
>> advantage of the (then just emerging) dataset collections feature.  However, 
>> it is not clear to me from the latest release notes if the data collections 
>> are now fully merged into master, or if I should continue to use the code in 
>> the dev branch to take advantage of bleeding edge code.  I would like to 
>> move back to the master branch as soon as feasible.
> 
> It is an ongoing effort - but the master branch as of now contains
> essentially everything in the dev branch
> https://github.com/galaxyproject/galaxy/tree/master. I need to put
> together some release notes for 15.07 before there can be an
> announcement of that but there is a few new collection related things
> in the release. In some senses though collections have been fully
> usable for over a year - and in some senses there is a lot of work
> left to do. Kind of depends on what you are doing.
> 
>> 
>> When running workflows over dataset collections I will frequently see errors 
>> like:
>> 
>> /bin/sh: 1: 
>> /home/galaxy/galaxy_old/database/job_working_directory/001/1216/galaxy_1216.sh:
>>  Text file busy
> 
> I don't think this is related to collections per se - I think it is
> probably more a file system problem - are you using a local job runner
> or a cluster manager? Is the file system mounted over a slow NFS
> connection?
> 
>> 
>> Which, from what I can tell, occurs when one process is trying to 
>> modify/delete a file open in another process.  While the error seems to be 
>> repeatable, it also seems random as the errors do not occur in the same 
>> places if I run the workflow multiple times.
>> 
>> Given that I am working from the dev branch I don't want to open/raise 
>> issues on features still in development.  But if this is unexpected then I 
>> can do some more investigating and file a proper bug report.
> 
> I would say report bugs in dev always - maybe check the existing ones
> on github and Trello first - but ideally we would like to catch bugs
> as early as possible and we don't usually commit half-baked code to
> dev - it should be bug free (though maybe missing features).
> 
> Hope this helps,
> -John
> 
>> 
>> Cheers,
>> Keith
>> 
>> ------------------------------
>> Research Associate
>> Department of Computer Science
>> Vassar College
>> Poughkeepsie, NY
>> 
>> 
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