Tag Archives: BowTie

Compile Bowtie2 on Windows 64 bit.

Bowtie 2 is a program that efficiently aligns next generation sequence data to a reference genome. However, the version distributed by the authors only compiles on POSIX platforms. These instructions will allow you to compile it on windows by downloading the Mingw64 tools and editing the make file before building the program. Instructions
  1. Download the Bowtie 2 source code. Extract the code to a location on your disk.
  2. Download the mingW64 compiler tools. These tools are much easier to use if they are downloaded as a package from this site: TDM Compiler Package. Be sure to select the TDM 64 bit version of the tools.
  3. Run the installer for the package. When prompted, select all of the available packages for installation.
  4. In explorer, navigate to where you unzipped the source code for bowtie. Find the file called Makefile and edit it. A great way to do this is to install the program notepad++. If notepad++ is installed, simply write click on the file and select “edit with notepad++”.
  5. Edit the file so that it knows it is compiling on Ming and Windows. To do this, insert # marks in front of all the if/else statements, so that lines 35 to 53 of the file look like this:
    # Detect Cygwin or MinGW
    #WINDOWS = 0
    #CYGWIN = 0
    #MINGW = 0
    #ifneq (,$(findstring CYGWIN,$(shell uname)))
    #WINDOWS = 1 
    #CYGWIN = 1
    # POSIX memory-mapped files not currently supported on Windows
    #BOWTIE_MM = 0
    #ifneq (,$(findstring MINGW,$(shell uname)))
    WINDOWS = 1
    MINGW = 1
    # POSIX memory-mapped files not currently supported on Windows
    BOWTIE_MM = 0
  6. Now edit the makefile so it points to a correct pthreads library. Edit line 76 so it reads as follows:
    PTHREAD_LIB = -lpthread
  7. Edit the file so that it compiles as 64 bit, change lines 121-132 to the following
    # Convert BITS=?? to a -m flag
    #ifeq (x86_64,$(shell uname -m))
    #ifeq (32,$(BITS))
    #BITS_FLAG = -m32
    #ifeq (64,$(BITS))
    BITS_FLAG = -m64
  8. Go to start->All Programs->MingGW64->MingGW Command prompt
  9. Navigate to the directory with the source code and make file by entering the cd command at the prompt, e.g.
    cd C:\Programs\bowtie2-2.0.6-source\bowtie2-2.0.6 
  10. Type “make” and hit enter.
  11. All done!
  12. Edit: One person had a comment on this, if this doesn’t work you may have to use teh MinGW shell. Edit: It has been pointed out that the BowTie2 team doesn’t use memory mapped files on windows. This might mean large genomes are less performant.