This tutorial is for building kallisto locally without root access. If you have root access and a package manager, please see the other tutorial.


We will assume you have the following installed:

  • A C++11 compatible compiler such as >= g++-4.8 (might work on g++-4.7, though untested)
    • Since this is very system specific, it is usually best to ask your administrator to install this. If not, you should search how to install it locally on your system.
  • zlib which is installed on most machines.
  • make which is also installed on most machines.


Since we will be installing things to your home directory, you should add $HOME/bin to your PATH if you haven’t already. This ensures that your shell knows where to look for binaries (cmake, kallisto, etc.). For this current session, run the following from your terminal:

export PATH=$HOME/bin:$PATH

Afterwards, place the same code into your shell startup file (e.g. one of ~/.bashrc, ~/.zshrc, etc.).

We’ll assume all downloads are in ~/Downloads. Make sure to change to the downloads directory before downloading each one of the source archives (*.tar.gz files)

Building and installing CMake

The easiest way to install CMake is from source. Head over to the CMake downloads page and get the latest “Unix/Linux Source” *.tar.gz file. Make sure to set the --prefix flag correctly, otherwise you won’t have permissions to install files at the default location.

tar -xf cmake*.tar.gz

cd cmake*

./configure --prefix=$HOME


make install

You should now have the most up-to-date installation of cmake. Check the version by typing:

cmake --version

Building and installing HDF5

Download the latest ‘configure’ version of HDF5. After extacting the tarball run configure with the following options:

./configure --disable-parallel --without-szlib --without-pthread --prefix=$HOME

Compile and install:


make install

All of the important HDF5 tools will be at $HOME/bin and libraries/include files at: $HOME/lib and $HOME/include.

Building and installing kallisto

Download the latest source tarball from GitHub, extract, and change directories:

wget ... (this is the GitHub ‘Source code (tar.gz)’ link)

tar -xf v0.4*

cd kallisto-*

Make a build directory and move to it

mkdir build

cd build

Since we put everything in $HOME, CMake is smart enough to look there and the following should work pretty seamlessly. Make sure you run CMake with the following command to install the binaries in $HOME:


Next, build and install:


make install

You will now have kallisto in $HOME/bin/kallisto. You might get an error:

./kallisto: error while loading shared libraries: cannot open shared object file: No such file or directory

If this is the case, make sure to add $HOME/lib to your LD_LIBRARY_PATH:


You may want to add this to your ~/.bashrc to ensure that it persists between sessions.