Work at SourceForge, help us to make it a better place! We have an immediate need for a Support Technician in our San Francisco or Denver office.


Bowtie 2 - beta 5 source file not found

  • Hi,
    I'd like to build Bowtie 2 - beta5 from source beacause I'm working on a Mac computer and only binaries for linux architecture are available on the corresponding download section of the Sourceforge site. According to the manual, I should have access to the Bowtie 2 sources from the same page, but the only package source I found (filename ending with is the one of Bowtie 1 - 0.12.7… Is there another way to obtain the same kind of file for Bowtie 2?

    By the way, I've also tried to use this binary file : but I've encountered errors when using bowtie2-build and bowtie2-align…

    Any help will be greatly appreciated.

  • I'm having the same kind of problem. Need to run Bowtie2 on Mac osx and the linux binary doesn't work.
    I get the error: cannot execute binary file
                              Died at ./bowtie2 line 69.

    I took a look at line 69 in the bowtie2 file (perl code), but it's beyond my programming knowledge.
    Does anyone know a fix for this or how to run Bowtie2 on Mac?


  • Hi again,
    Apparently, contrary to what is mentioned in the Bowtie 2 manual, the source package for Mac osx doesn't end in Instead, it corresponds to the following file:

    Then all you have to do is to follow the manual's instructions: "unzip the file, change to the unzipped directory, and build the Bowtie 2 tools by running GNU make (usually with the command make, but sometimes with gmake) with no arguments "
    And it should work fine.