Hi Kraig, There are instructions for setting up your shell environment and building the source, along with a few common problems and their solutions, in the source tree in the file: kent/src/product/README.building.source
This is also online, here: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/product/README.building.source If you have further questions, please feel free to send them back to this list ([email protected]). -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/17/10 08:04, Kraig Stevenson wrote: > I'm having some difficulty building the source utilities on my Mac. The > online resource at UCSC is for building and installing on Linux/Unix > systems. Specifically, I am using version 10.6.5. I know this is Unix-based, > but is there a way to build the source on a Mac? > > Thanks! > > -Kraig > > On Tue, Nov 16, 2010 at 7:54 PM, Mary Goldman <[email protected]> wrote: > >> Hi Kraig, >> >> You can get chainSwap utility as a part of our source downloads. >> You can find instructions about downloading and installing kent source >> utilities here: >> >> http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads >> http://genome.ucsc.edu/admin/jk-install.html >> >> With the actual source download residing here: >> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip >> >> I hope this information is helpful. Please feel free to contact the mail >> list again if you require further assistance. >> >> Best, >> Mary >> ------------------ >> Mary Goldman >> UCSC Bioinformatics Group >> >> >> >> On 11/16/10 2:29 PM, Kraig Stevenson wrote: >> >>> To whom it may concern: >>> >>> My name is Kraig Stevenson, and I am a PhD student in bioinformatics at >>> the >>> University of Michigan. I would like to request the chainSwap utility. >>> >>> Thank you very much! >>> >>> -Kraig >>> >>> ---------- Forwarded message ---------- >>> From: Jim Kent<[email protected]> >>> Date: Tue, Nov 16, 2010 at 3:30 PM >>> Subject: Re: Reverse chain files for LiftOver tool >>> To: Kraig Stevenson<[email protected]> >>> >>> >>> In general you will want to generate a separate chain file for the >>> reverse. >>> I _think_ you'll end up with just a 5% less good result if you basically >>> swap the target and query sequences in the chain. We have a chainSwap >>> utility at UCSC that will do that. If this is the route you decide to >>> take, >>> please contact [email protected] to get the utility. It'd be best if >>> you >>> got in contact with whoever generated the chain file in the first place >>> though. >>> >>> Take care, >>> Jim >>> >>> On Nov 16, 2010, at 11:28 AM, Kraig Stevenson wrote: >>> >>> Hello Dr. Kent, >>> >>> My name is Kraig Stevenson, and I am a bioinformatics PhD student at the >>> University of Michigan. I have extensively used your LiftOver tool to go >>> between species, and I currently have a chain file that lifts coordinates >>> from one (non-sequenced) species to a (sequenced) species (this was given >>> to >>> us by a collaborator). Now I would actually like to go in the opposite >>> direction, but I am not sure how to go about this. Is there a way to >>> reverse >>> the chain file so that the LiftOver tool could accomplish this task? Could >>> the LiftUp tool be used in this situation? >>> >>> Any advice you might have would be greatly appreciated. >>> >>> Best regards, >>> >>> -Kraig >>> >>> >>> >> >> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
