This page was last updated on Friday, 30-May-2014 08:10:18 CDT

Installation notes for BEDOPS version 2.4.2 (April 10, 2014)

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Prerequisites

None

Installation

1. $ cd /programinstallers/
2. $ ver=2.4.2
3. $ wget -N https://github.com/bedops/bedops/releases/download/v$ver/bedops_linux_x86_64-v$ver.tar.bz2
4. Downloads to a crazy file name, fix that
   $ mv *filename=bedops_linux_x86_64-v$ver.tar.bz2* bedops_linux_x86_64-v$ver.tar.bz2
5. Extracts to a generic bin directory
   $ tar -jxvf bedops_linux_x86_64-v$ver.tar.bz2
6. $ cp -puv bin/* /usr/local/bin/

   `bin/bam2bed' -> `/usr/local/bin/bam2bed'
   `bin/bam2starch' -> `/usr/local/bin/bam2starch'
   `bin/bedextract' -> `/usr/local/bin/bedextract'
   `bin/bedmap' -> `/usr/local/bin/bedmap'
   `bin/bedops' -> `/usr/local/bin/bedops'
   `bin/closest-features' -> `/usr/local/bin/closest-features'
   `bin/gff2bed' -> `/usr/local/bin/gff2bed'
   `bin/gff2starch' -> `/usr/local/bin/gff2starch'
   `bin/gtf2bed' -> `/usr/local/bin/gtf2bed'
   `bin/gtf2starch' -> `/usr/local/bin/gtf2starch'
   `bin/psl2bed' -> `/usr/local/bin/psl2bed'
   `bin/psl2starch' -> `/usr/local/bin/psl2starch'
   `bin/sam2bed' -> `/usr/local/bin/sam2bed'
   `bin/sam2starch' -> `/usr/local/bin/sam2starch'
   `bin/sort-bed' -> `/usr/local/bin/sort-bed'
   `bin/starch' -> `/usr/local/bin/starch'
   `bin/starchcat' -> `/usr/local/bin/starchcat'
   `bin/starchcluster' -> `/usr/local/bin/starchcluster'
   `bin/starchcluster.gnu_parallel' -> `/usr/local/bin/starchcluster.gnu_parallel'
   `bin/unstarch' -> `/usr/local/bin/unstarch'
   `bin/vcf2bed' -> `/usr/local/bin/vcf2bed'
   `bin/vcf2starch' -> `/usr/local/bin/vcf2starch'
   `bin/wig2bed' -> `/usr/local/bin/wig2bed'
   `bin/wig2bed_bin' -> `/usr/local/bin/wig2bed_bin'
   `bin/wig2starch' -> `/usr/local/bin/wig2starch'

7. Cleanup
   $ rm bin/* && rmdir bin