Ok, I'll be very happy to see what you've accomplished there.  I will read 
through what you've done when I return from vacation in a week!

A key need is to have whatever data comes in show up as linked data in one's 
history to avoid server overhead; a second objective was to not need to modify 
existing workflows - as long as they could work of data in history that is 
typed appropriately.  So your 'select type' solution sounds intreguing!

And certainly interested in your use of git - I tried using git, using a 1-line 
fasta data format, but git seemed to choke on protein fasta files?  And did it 
run into performance problems with larger files?  That was my experience.  I 
think I read its authors say that its upper limit was 15gb.  That was the 
motivation for writing a simple key-value master file diff system that seems to 
have the same I/O as git on smaller files, but more reliable for the fasta data 
case, and no problems with larger files - it outputs a new version in the same 
time it takes to read a master file.  It has drawbacks though - incoming data 
to compare master with must be sorted in 1 line fasta format first.

Thanks for your input; looking forward to your project writeup...


Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for 
Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Saturday, August 23, 2014 12:17 AM
To: Dooley, Damion; galaxy-dev@lists.bx.psu.edu
Cc: Hsiao, William
Subject: Re: [galaxy-dev] Concept for a Galaxy Versioned Fasta Data Retrieval 

Hi Damion,

the idea sounds fantastic!
Can we go a step further and use a specific datatype that keeps entire
fasta files versioned and the user can choose which version he wants to
use, in any tool? Please have a look at my talk at GCC2012. Maybe you
are interested in the (old) patches. I would be very interested to
restart this old project.


Am 23.08.2014 um 03:24 schrieb Dooley, Damion:
> We are about to implement a fasta database (file) versioning system as a 
> Galaxy tool.  I wanted to get interested people's feedback first before we 
> roll ahead with the prototype implementation.  The versioning system aims to:
>    - Simple makeblastdb or bowtie-build commands, or more specific workflows 
> that include dustmasker etc can be implemented.
> Does this sound attractive?

I think all of the use cases are covered by the old project mentioned
above. But I did not create a new tool I have created a new 'select
type' everyone can use in all tools. It was using git underneath (yeah,
I have the entire PDB in git and it is working fine :)) but we can
probably change git with a database if you like.

To answer your question: Yes, very attractive!

> We're hoping such a vision could handle Fasta databases from 12mb to e.g. 
> 200Gb (probably requires makeblastdb in parallel at that scale).
> Preliminary work suggests this project is doable via the Galaxy API without 
> galaxy customization - does that sound right?!

Yes, as long as the User has an API key.

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