Question: BEDOPS installation on MAC
0
gravatar for MK2000
4 days ago by
MK20000
MK20000 wrote:

Hello!

I am very new to programming and working with omics data in general, but I am trying to convert a VCF file to a BED file in my terminal on MacOS. I was interested in downloading the BEDOPS tool package and using the vcf2bed command. I then downloaded the latest version of BEDOPS, per instructions on their website, and my computer said the download was successful. However, when I go to use the vcf2bed command in my terminal, it is not recognized! Is this because the BEDOPS package downloaded somewhere other than my current directory? If so, how can I make BEDOPS work in the directory I am in?

Many thanks for any help!

bedops assembly • 102 views
ADD COMMENTlink modified 4 days ago by Alex Reynolds26k • written 4 days ago by MK20000
1
gravatar for Alex Reynolds
4 days ago by
Alex Reynolds26k
Seattle, WA USA
Alex Reynolds26k wrote:

If you're using Mac OS X, download the installer package from the Releases page. Unpack and run the installer and follow its instructions. Then open a Terminal session and you should be able to run BEDOPS tools.

ADD COMMENTlink written 4 days ago by Alex Reynolds26k

Hello Alex,

Thanks for your comment. I am able to run through the installer package from the Releases page with success (or though it seems). However, the vcf2bed command is still not recognized when I go to use it in terminal. I feel the error could be with this step in the installation:

"BEDOPS binaries and scripts will be installed in /usr/local/bin and this installer will therefore need to ask you to grant administrator-level access to your startup volume. You should be able to run these binaries in a command-line environment without any extra work on most workstations. If not found, be sure that /usr/local/bin is in your shell's PATH environment variable, and append it, if necessary."

However, I've just been ignoring this through the installation since I'm not sure entirely sure what the last step means. Is it this message that means BEDOPS may not be running in my current directory?

ADD REPLYlink written 4 days ago by MK20000

What do you get when you run echo $PATH?

ADD REPLYlink written 4 days ago by Alex Reynolds26k

PATH is an very basic element of Unix. I strongly recommend you make yourself familiar with it.

ADD REPLYlink written 4 days ago by ATpoint11k
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