[InterMine Dev] Galaxy Export ...

Alex Kalderimis alex at intermine.org
Wed Mar 27 19:04:00 GMT 2013

Currently the upload tool we are using in galaxy main just happens to be 
called flymine, but is completely generic. We didn't even write it I believe. 
It can, and should be renamed "intermine upload" or something similar, and I 
will speak to the Galaxy crew about that next week. 

We should also be able to have tools for each group (although that does sound 
like a lot of pointless duplication). Let me know how important it is to get 
your branding up there.

All best,


On Wednesday 27 March 2013 18:54:56 Jayaraman, Pushkala wrote:

I see in the box you’ve copied:
FlyMine ==> Flymine
Metabolic ==> Flymine
modMine ==> Flymine
Rat ==> [broken]
MouseMine ==> Flymine
YeastMine ==> YeastMine
Rat shows broken link.. 
Do let me know what I can do to fix this.. if this is an existing feature that 
just needs a little fixing I may be able to fix it so that it isn’t broken for 
you anymore.. 
From: dev-bounces at intermine.org [mailto:dev-bounces at intermine.org] On Behalf 
Of Howie Motenko
Sent: Wednesday, March 27, 2013 1:51 PM
To: dev at intermine.org
Subject: [InterMine Dev] Galaxy Export ...
We've got the Galaxy export up and running.  But a funny little thing happens.
First let me define (in my own words) the galaxy stages as represented in the 
history column (far right-hand side) …
 1. The data is queued to galaxy => a grey box with a title (currently 
 2. The data is processed by galaxy => a yellow box with a title of the data.
 3. The data is available [or an error] for galaxy's tools => a green box [red 
box for error].
Okay now here's the wiggy thing … During the first stage in the grey box the 
data is displayed "Flymine", though it comes from 'MouseMine'.  How can we 
change it to read 'MouseMine'?
As a point of reference:
Mine  ==> Grey titled displayed
FlyMine ==> Flymine
Metabolic ==> Flymine
modMine ==> Flymine
Rat ==> [broken]
MouseMine ==> Flymine
YeastMine ==> YeastMine
And there's the interesting point YeastMine actually displays 'YeastMine' in 
the grey box.  We'd like to do that too.
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Software Developer
Department of Genetics
University of Cambridge
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