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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