On Wed, Feb 29, 2012 at 5:14 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> Hi Carlos,
> You can certainly add support for a sqlite database datatype to your local
> galaxy instance.  As you say, it may be no more complex / fragile than h5
> or other binary datatypes - I've not gone far enough down the analysis path
> to provide good reasons why it may or may not be reasonable, so perhaps
> I spoke too soon.  If you have questions about how to add support for new
> datatypes, see our wiki at http://wiki.g2.bx.psu.edu/Admin/Datatypes.
> Thanks!
> Greg Von Kuster

My impression is that as long as you treat it as a write once-data-read-
many file using an SQLite3 database in Galaxy could work. By that
I mean any tool can create and modify SQLite3 files as some of its
output files, and any tool can also have any number of SQLite3 files
as inputs - but must treat them as read only.

The trouble will start if you actually use a pre-existing SQLite3 file like
a database and make changes to it. That will break Galaxy's assumptions
about how to reproduce the file for workflows etc.

Perhaps Galaxy should actively preempt the possibility of tools editing
old data files by making all the history data files read only right after the
tool creating them has finished? This could catch some existing 'naughty'
tools editing things they are not meant to.


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