to compile these from source you'll want to grab the BLAT source code from 
here: http://users.soe.ucsc.edu/~kent/src/





On Aug 12, 2011, at 6:38 AM, Peter Cock 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?
> 
> 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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--
Glen L. Beane
Senior Software Engineer
The Jackson Laboratory
(207) 288-6153


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