sort-bed command not found

Question

I have the following code " not mine"

wget -qO- http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp142Common.txt.gz \
    | gunzip -c - \
    | cut -f2,3,4,5,10 - \
    | sort-bed - \
    > hg19.snp142.bed

when I run it on terminal it gave me the following error

sort-bed: command not found

how to fix it?

Answer 1

sort-bed is contained in BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit, which can be easily installed following these steps:

1. Download the current 64-bit package for Linux from Github BEDOPS Releases. 32-bit binaries can be built via source code by adjusting compile-time variables, see here.

2. Extract the package to a location of your choice. In the case of 64-bit Linux:

   tar jxvf bedops_linux_x86_64-vx.y.z.tar.bz2
   

   Replace x, y and z with the version number of BEDOPS you have downloaded.

3. Copy the extracted binaries to a location of your choice which is in your environment’s PATH, e.g. /usr/local/bin:

   cp bin/* /usr/local/bin
   

   Change this destination folder, as needed.