[galaxy-dev] Misc file types and odd intermediate/end-point file types.

[Cameron Jack]

Dear Dev Team,

My program that I'm trying to integrate with Galaxy relies on SQLite 
databases to hold gene annotation information throughout multiple stages 
of processing. Given that the .db files produced by SQLite are not one 
of the standard data file types, is there any provision for a misc 
binary type for either a) data upload or b) intermediate processing? I 
find a lack of a misc 'binary' format surprising considering I can 
rename any file as .txt and it will upload as 'txt' format just fine 
(and presumably be loaded by my program within Galaxy just fine too).


Similarly, my program produces image files (data plots) in any of the 
standard image file formats - PNG, PDF, JPEG. Would users be able to 
download these from Galaxy once my program has produced them?


Any ideas on how to get this to work would be much appreciated.

Kind regards,
Cameron


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[galaxy-dev] Tool tests

[Cameron Jack]

Hi, I hope I'm writing to the right area (if not, please point me in the 
right direction and I'll go on my way).


I have a set of tools that our team have built and been using for 
functional genomics analysis, which I would like to integrate into Galaxy.


My first concern is with the tests. Our code is unit tested but one 
script is tasked with downloading gene sets from Ensembl. We have a 
local copy of much of the Ensembl DB (5TB worth) and even this is fairly 
slow to pull from (5-10 mins). Pulling from the publicly available 
Ensembl site would be horrifically slow. Since it's stated here: 
http://wiki.galaxyproject.org/Admin/Tools/Writing%20Tests that 
functional tests are required, I'm looking for suggestions as to how to 
meet this requirement without taking up an hour of the test runner's 
time (for one tool).


My second question is if a file is produced by a script and given a 
specific name based on its inputs, how should I (if at all) define the 
output of this script.


My last question is how much functional testing is required?. I have a 
script here whose job is to produce plots of data. There are about 30 
command-line options and many of these have multiple choices available 
to them. Do I need to provide functional tests for every one of these? I 
can imagine having to provide 100 PNG files to compare my output again


I have searched for answers to the above (made much more tricky thanks 
to Samsung), I don't wish to waste anyone's time.


Many thanks in advance,
Cameron


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