On Fri, Aug 12, 2011 at 11:38 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> 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?

Would I be right to guess the Penn State cluster is all 64bit Linux?
Some of our cluster nodes are just 32bit, so I wanted to grab the
32bit binaries for faToTwoBit, twoBitToFa and liftOver - but this
folder just contains liftOver at the moment:


I guess I'll have to compile faToTwoBit and twoBitToFa from

> ..
> 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?

That's fine for faToTwoBit and twoBitToFa, but...

What about the liftOver tool? This is under the hg top level
folder, and thus is NOT licensed for commercial users -
only for personal, academic, and non-profit use. How is
Galaxy able to use this tool on the public Penn State server?



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