The kallisto GitHub repository is here. Source code can also be downloaded from the download page. Currently, kallisto can be built on Linux, Mac, and Rock64. If you are compiling kallisto on the Rock64 (or equivalent ARM64 processor architecture) follow these steps. If building on Mac, we suggest using a package manager such as Homebrew to download dependencies. Homebrew is easily installed by copying and pasting the command below at a terminal prompt:

ruby -e "$(curl -fsSL"

Other dependencies are included, or can be installed using package managers on the system. Instructions for building kallisto from source without a package manager are here.


  • A 64-bit operating system
  • g++ version >= 4.8
  • CMake version >= 2.8.12
    • Mac: brew install cmake
    • Ubuntu: sudo apt-get install cmake
    • CentOS: sudo yum install cmake
  • zlib (should be installed on OSX >= 10.9)
    • Mac: Should be installed by default
    • Ubuntu: sudo apt-get install zlib1g-dev
    • CentOS: sudo yum install zlib-devel
  • autoconf
    • Mac: brew install autoconf
    • Ubuntu: sudo apt-get install autoconf
    • CentOS: sudo yum install autoconf
  • HDF5 C library version >= 1.8.12
    • Mac: brew install hdf5
    • Ubuntu: sudo apt-get install libhdf5-dev
    • CentOS: sudo yum install hdf5-devel


kallisto is hosted on GitHub. The source code can be obtained by cloning the repository as follows:

git clone


Begin by moving to the source directory:

cd kallisto

Make htslib

Run autoconf on ext/htslib: (note, this only needs to be done once, not when you recompile)

cd ext/htslib



cd ../..

For old Linux systems, if you get an error reporting thread_pool.c:658:38: error: ‘PTHREAD_MUTEX_RECURSIVE’ undeclared (first use in this function)

you might need to make htslib using this command in the htslib folder

make -j CFLAGS=-D_GNU_SOURCE lib-static

Build kallisto

Make a build directory and move there:

mkdir build

cd build

Run cmake:

cmake ..

Build the code:


The kallisto executable is now located in build/src. To install kallisto into the cmake install prefix path type:

make install


The kallisto source code package comes with a small test transcriptome and read files that can be used to test that the package was compiled and installed correctly. The Getting started page provides a complete description of how to run kallisto on these files.