Great -- it seems support for batch processing of many files was recently added. See "Workflows & Multiple datasets" at . Many thanks to the Galaxy developers, and in this case Martijn Vermaat, who I think wrote this feature.

Now, to return to my second question - is there a Reduce for this Map?


On 24-Jul-11 09:19, Andrew Straw wrote:

(Warning: Galaxy newbie here.)

I'd like to run a series of galaxy tools repeatedly on multiple input
files. In other words, I have input data files [data1, data2, ...,
dataN] and I want to apply [step1, step2] to each of these files to
produce [output1, output2, ..., outputN]. I know that I can automate the
application of the multiple steps to a single input file as a workflow,
but is there any way to automate running a workflow multiple times on
multiple inputs through the Galaxy web interface? (I see the scripts in
scripts/api, but I'm looking for something entirely driven by the web
user interface.)

For a second question, is there a recommended way of combining then
merging the results (e.g. from multiple workflows) into a single file?

The use case for this is that we're doing experiments on lots of
individual flies from several genotypes and we want to analyze data from
our individual fly experiments but then pool results across flies from
the same genotype and compare with other genotypes. I imagine this is
pretty similar to what a lot of people are doing, but somehow I'm not
getting how this might be done with Galaxy.


Andrew D. Straw, Ph.D.
Research Institute of Molecular Pathology
Vienna, Austria

The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

Reply via email to