Troubling installing kent-core and oligoMatch

[Erin Brettmann]

Hello,

 

I’m trying to install the kent-core package (specifically for oligoMatch) on my Mac (OSX-arm64). I attempted to clone from Github:

     git clone https://github.com/ucscGenomeBrowser/kent-core.git

     cd kent-core

     make

 

It did some things and then gave the error message:

     hmac.c:11:10: fatal error: 'openssl/hmac.h' file not found

   11 | #include "openssl/hmac.h"

      |          ^~~~~~~~~~~~~~~~

1 error generated.

 

I then tried to download the oligoMatch program directly from hgdownload:

     rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/macOSX.arm64/oligoMatch ./

 

The file downloads but I cannot use it.

                oligoMatch path_to_oligo.fa path_to_reference.fa path_to_output.bed

                                zsh: command not found: oligoMatch

 

Do you have any suggestions on how to make either of these approaches work? How to address the error from using make or how to install the program I’ve already downloaded via rsync?

 

Thank you,

 

Erin Brettmann, PhD (she/her)

Senior Scientist

Genome Editing

 

MilliporeSigma

A business of Merck KGaA, Darmstadt, Germany

 

2909 Laclede Ave. | Saint Louis, MO | 63103 | USA

Phone: +1 (314) 771-5765 x63142437

www.sigma-aldrich.com

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[Maximilian Haeussler]

Hi Erin,

our code requires openssl, and OSX doesn't include openssl anymore (I believe). Are you using brew? If so, can you run

$ brew install openssl

to install this library and try the "make" command again.

To run the OSX binary, which is probably easier, I think OSX doesn't include "." in the PATH variable, so you have to run it like this:

./oligoMatch

Also, I'm curious what it is that you're trying to do. Our oligoMatch tool is not an aligner, and can be used for many things, and I'm curious if you're looking for primers, miRNAs, CRISPR targets or something else?

best,

Max

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[Hiram Clawson]

Try running the command:

./oligoMatch

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