Question: Programs of UCSC utilites
0
gravatar for IP
4.1 years ago by
IP700
Denmark/University of Copenagen
IP700 wrote:

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!

ADD COMMENTlink modified 2.2 years ago by sschmeier80 • written 4.1 years ago by IP700
1

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.

ADD REPLYlink written 4.1 years ago by Devon Ryan96k
2
gravatar for Maximilian Haeussler
4.1 years ago by
UCSC
Maximilian Haeussler1.3k wrote:

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

ADD COMMENTlink written 4.1 years ago by Maximilian Haeussler1.3k

UCSC virtual machine is downloadable from UCSC genome store here.

ADD REPLYlink written 4.1 years ago by genomax90k
4
gravatar for Alex Reynolds
4.1 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

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

$ brew install homebrew/science/kent-tools
ADD COMMENTlink written 4.1 years ago by Alex Reynolds30k
1
gravatar for Alex Reynolds
4.1 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

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.

ADD COMMENTlink written 4.1 years ago by Alex Reynolds30k
0
gravatar for sschmeier
2.2 years ago by
sschmeier80
New Zealand
sschmeier80 wrote:

Use conda and bioconda:

conda install ucsc-genepredtogtf ucsc-gtftogenepred
ADD COMMENTlink written 2.2 years ago by sschmeier80
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