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
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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153
On Fri, Aug 12, 2011 at 12:28 PM, Glen Beane <Glen.Beane@jax.org> wrote:
to compile these from source you'll want to grab the BLAT source code from here: http://users.soe.ucsc.edu/~kent/src/
It looks like these are two different URLs for the same place, only one server shows the README file at the top and the other doesn't: http://users.soe.ucsc.edu/~kent/src/ http://hgwdev.cse.ucsc.edu/~kent/src/ The UCSC website does seem like a maze ;) Peter
On Aug 12, 2011, at 7:42 AM, Peter Cock wrote:
On Fri, Aug 12, 2011 at 12:28 PM, Glen Beane <Glen.Beane@jax.org> wrote:
to compile these from source you'll want to grab the BLAT source code from here: http://users.soe.ucsc.edu/~kent/src/
It looks like these are two different URLs for the same place, only one server shows the README file at the top and the other doesn't:
http://users.soe.ucsc.edu/~kent/src/ http://hgwdev.cse.ucsc.edu/~kent/src/
The UCSC website does seem like a maze ;)
Peter
I should have read your email a little more clearly! I read "That just contains pre-compiled binaries - but there is no sign of the source code or a licence file." and thought "hey I know where the source is" and then replied without ever getting to the part where you found http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/utils/twoBitToFa/ Yes, it is definitely not obvious where to go to get these tools -- I remember I had to dig a while to find faToTwoBit -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153
participants (2)
-
Glen Beane -
Peter Cock