I get an error when trying to run through the steps in "Introduction to variant calling"

Question

[pmiller]

Hello, I am trying to learn more about variant calling so I'm looking through the new handbook sections. I am trying to run this command in my bioinfo environment (from the tutorial steps):

dwgsim -N 1000 genome.fa sim

But I get:

-bash: dwgsim: command not found

I installed programs on my Mac as instructed at the beginning of the new handbook. It was noted that the Mac version of the install might require some additional programs be added in another way. Is that the issue here?? Or, something else.

Oh, I can use wgsim.

Thanks

Answer 1

[ATpoint]

Your command is not in PATH. Please google what PATH is in Unix and how to add something to it.

Answer 2

[pmiller]

The path isn't the problem, I did test that just in case this one command needed the full path. I'm running all the commands in the "bioinfo" environment in the folder where I put the tutorial files and everything else is working.

I checked and the problem is that this program does not install when doing the bioinfo setup for Mac OSX. I had to install it separately.

[Ram]

this program does not install

What do you mean by that?

EDIT: I opened an issue for this. Thank you once again!

I see that the conda config does not list dwgsim. Please open an issue on the issue tracker. Thank you for catching this bug!