Monday, 4 July 2011

Compiling BEDTools on Ubuntu 10.04 LTS - the Lucid Lynx

You will need these libraries

sudo apt-get install g++
sudo apt-get install zlib1g-dev

after which, it is a simple
$ make clean
$ make all[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
- Building in src/utils/lineFileUtilities
  * compiling lineFileUtilities.cpp

- Building in src/utils/bedFile
  * compiling bedFile.cpp

- Building in src/utils/bedGraphFile
  * compiling bedGraphFile.cpp

- Building in src/utils/tabFile
  * compiling tabFile.cpp

- Building in src/utils/genomeFile
  * compiling genomeFile.cpp

- Building in src/utils/gzstream
g++ -Wall -O2 -c -o ../../../obj//gzstream.o gzstream.C -I.




  1. Thanks for posting this hint! The files did extract in the bin folder. However, when I try to run any of the executables, I get a "command not found" error. Any ideas, Kevin?

  2. where are the full location of the binaries? did you try to run them when in the same directory?

    what's the command and where did you run the command?

  3. I am in the directory ~/BEDTools-Version-2.12.0/bin$ where all the executables are. When I type either of them, e.g. fastaFromBed I get the "command not found" error. Thanks!

  4. Hmm did you try ./fastaFromBed ?

  5. You're a genius! Thanks so much!


Datanami, Woe be me