installing blat for homer on os x

Question

[tonja.r]

I have downloaded blat from here. I have also added in to executable path. PATH=$PATH:/Users/katja/Desktop/MyDocuments/Programms/blat

But I can run the program only from the folder where it is situated and only by typing ./blat and not simple blat, therefore homer does not recognize it. What should I do in order to be able to run a program just blat.

Answer 1

[Alex Reynolds]

When you say "recognize", does that mean that Homer doesn't like the version it finds (too old?), or that it can't find blat at all? What is the error message?

Run which blat and echo $PATH to double-check that 1) blat can be found and 2) that the version that is running is from the specific folder you specify.

One tip when modifying PATH is to put your custom folders first in line, since you might already have some other, older version of the binary in question. When your shell looks for a binary, it will search those custom folders, before all others.

[tonja.r]

which blat gave nothing.

echo $PATH:

/Users/katja/Desktop/MyDocuments/Programms/blat:/Users/katja/Desktop/MyDocuments/Programms/homer/bin/:/Users/katja/Desktop/MyDocuments/Programms/samtools-0.1.19/:/Users/katja/Desktop/MyDocuments/Programms/ghostscript-9.16/bin/:/Users/katja/Desktop/MyDocuments/Programms/weblogo/:/Users/katja/Desktop/MyDocuments/Programms/blat

Homer does not find beat at all.So, I still do not understand what is wrong.

[Alex Reynolds]

Is /Users/katja/Desktop/MyDocuments/Programms/blat a folder called blat, which then contains an executable called blat, or is that part of PATH the actual executable itself? You should only put folders into PATH.

Answer 2

[g.corey.shan]

Here might be a solution: https://shanguangyu.com/articles/install-blat-on-mac-with-one-liner-command/