Programs of UCSC utilites

Question

[IP]

Hi!

I need to install two programs from UCSC utilites: - genePredToGtf - gtfToGenePred

I have tried to install them, and to install the whole package and I am not able to install them. Does anyone know a good tutorial in order to install them?gtfToGenePred

Thank you!

[Devon Ryan]

What operating system are you using? For Linux you can just download the executables from UCSC. That might work for a Mac too. For Windows, find someone with a Mac or Linux computer.

Answer 1

[Maximilian Haeussler]

Download the binaries for Linux from here: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/

If you're on OSX, download the tools from here: http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/

If you're on Windows, get UCSC's virtual machine, run it on linux and type "gbibAddTools": https://genome.ucsc.edu/goldenpath/help/gbib.html

[GenoMax]

UCSC virtual machine is downloadable from UCSC genome store here.

Answer 2

[Alex Reynolds]

If you're running OS X and Homebrew, you can run the following to install Kent-tools:

$ brew install brewsci/bio/kent-tools

Note: The following cask appears to be deprecated and does not appear to work:

$ brew install homebrew/science/kent-tools

Answer 3

[Alex Reynolds]

As another option, you could clone the Github repository and compile tools directly:

$ git clone https://github.com/ENCODE-DCC/kentUtils.git
$ cd kentUtils
$ make
...

Etc.

Answer 4

[sschmeier]

Use conda and bioconda:

conda install ucsc-genepredtogtf ucsc-gtftogenepred