On Jun 5, 2015, at 2:10 PM, David Kelly <davidkelly(a)uchicago.edu> wrote:
I am able to manually convert from a->b and then separately b->c, but not directly
from a->c. I'm still thinking about how to approach this as well, but I'll
share my thoughts so far.
Does Galaxy automatically do the conversions for you in the workflow editor? For example,
if you have a tool A that produces format 'a' and another tool B that consumes
format 'b' you should be able to drag the "noodle" from A to B and
Galaxy will do an implicit format conversion. If this is working for you then someone
from the Galaxy team will have to jump in. If Galaxy is not doing implicit format
conversions then it likely means your datatype(s) are not fully defined. I didn't get
the implicit format conversion working properly until I implemented the format sniffers.
In our use case, we have a collection of climate tools we'd like
to use. The tools are written by different groups, so most use their own file formats.
Ideally we would like users to be able to upload their data in any of these file formats
and use all tools without having to explicitly convert their data.
Let's say there are 10 climate datatypes. My understanding is that in order to
achieve this kind of interoperability, I'd have to write 90 converters.
If Galaxy could chain converters together, I could write 1 converter per datatype and
chain them together like this:
a -> b -> c -> d -> e -> f -> g -> h -> i -> j -> a
Another scenario I've been thinking about is picking one data type to be the
'standard'. Let's say it's 'a' in this example. You could write 18
a->b, a->c, a->d,...
b->a, c->a, d->a,...
This is what we do. We have a standard "pivot format" then converters from the
other formats to/from the pivot format.
Then suppose you wanted to plug a 'd' file into a 'c' tool. You could
first manually convert d->a, then use the automatic conversion for a->c. Not fully
automatic, but not too bad.
On Thu, Jun 4, 2015 at 5:20 PM, Keith Suderman <suderman(a)anc.org> wrote:
We just got it working for the single conversions, that is, getting Galaxy to
automatically convert from a -> b when needed. Are you able to do the conversion, i.e
a -> b and b -> c individually?
We are just coming to a similar use case and I'm definitely interested in how you
make out, even if I can't be much help.
On Jun 3, 2015, at 4:15 PM, David Kelly <davidkelly(a)uchicago.edu> wrote:
> Suppose I have three custom datatypes defined: a, b, and c
> I have a datatype converter that converts from a -> b
> I have a datatype converter that converts from b -> c
> Can I then send 'a' files as input into tools that accept type 'c'?
> This doesn't seem to work in my test case, but I thought it might be worth
asking to see if anyone has tried this before. Thanks!
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Department of Computer Science
Department of Computer Science