Hi all,

I recently started trying "Extract Genomic DNA" which requires
faToTwoBit, which wasn't listed on the dependencies page
(fixed now), http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies

See also:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-August/006366.html

In updating the wiki I've assumed faToTwoBit comes from the same
place as twoBitToFa, where the link given is simply:
http://hgdownload.cse.ucsc.edu/admin/exe/

That just contains pre-compiled binaries - but there is no sign
of the source code or a licence file. Are you just using these
binaries?

I feel like I've been getting lost in the UCSC website...

I eventually found Jim Kent's pages, which appears to host
the twoBitToFa source code along with other tools like BLAT,

http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/utils/twoBitToFa/

The log files hinted at there being a git repository, which
I found here, http://genome-source.cse.ucsc.edu/
http://genome.ucsc.edu/admin/git.html

The licensing is murky, apparently free to use for personal,
academic, and non-profit use - but no mention about potential
redistribution or modification rights:
http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/README

> ... All files are copyrighted, but license is hereby granted
> for personal, academic, and non-profit use.  license is
> also granted for the contents of the top level lib, inc and
> utils directories for commercial users. ...

Have the Galaxy team made special arrangements to license
faToTwoBit for use on the Penn State public server, or is this
fine because faToTwoBit is under the top level utils directory?

Have I overlooked some general page introducing the Kent
tools like faToTwoBit? If such a page exists, could it be linked
to from the Galaxy Tool Dependencies page?

Thanks,

Peter
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