Dear Galaxy developers,

I hope you could help me with the following issue.
I wish to use galaxy tools in our AMADEUS motif finding software:
AMADEUS helps many users who wish to find motifs in their sequences.
AMADEUS has 2 limitations:
1. It can find motifs vs all organism's genome.
2. If the user don't want to find motif vs all organism's genome then The
user itself will have to supply the sequences for the motif finding
according to his chipSeq peaks he got.

We would like that the user won't be troubled with the second limitation by
adding locally\cloud Galaxy that downloads to AMADEUS the relevant
sequences (~3000 sequences)
according to the peaks locations from a BED file supplied by the user.

As I see it - the galaxy installation will have to follow the objectives:
1. Work on windows OS.
2. Can be installed in the user computer by a script in AMADEUS
3. downloading time of the relevant sequences (~3000) won't take above 1-2

I will appreciate if someone of you will guide me with the procedure and
advise me with the best way to work with Galaxy-AMADEUS interface.


Tom hait
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