Question: Programs of UCSC utilites
0
gravatar for IP
3.5 years ago by
IP690
Denmark/University of Copenagen
IP690 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 19 months ago by sschmeier80 • written 3.5 years ago by IP690
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 3.5 years ago by Devon Ryan94k
2
gravatar for Maximilian Haeussler
3.5 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 3.5 years ago by Maximilian Haeussler1.3k

UCSC virtual machine is downloadable from UCSC genome store here.

ADD REPLYlink written 3.5 years ago by genomax78k
4
gravatar for Alex Reynolds
3.5 years ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k 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 3.5 years ago by Alex Reynolds29k
1
gravatar for Alex Reynolds
3.5 years ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k 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 3.5 years ago by Alex Reynolds29k
0
gravatar for sschmeier
19 months ago by
sschmeier80
New Zealand
sschmeier80 wrote:

Use conda and bioconda:

conda install ucsc-genepredtogtf ucsc-gtftogenepred
ADD COMMENTlink written 19 months ago by sschmeier80
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 863 users visited in the last hour