1# kallisto installation
2
3Requirements
4------------
5- CMake version >= 2.8.12
6    - Can be installed via homebrew: `brew install cmake`
7- zlib (should be installed on OSX >= 10.9)
8- HDF5 C libraries
9
10Installation
11------------
12
131. First clone the repository:
14
15    ```
16    git clone https://github.com/pachterlab/kallisto.git
17    ```
18
191. Move to the source directory:
20
21    ```
22    cd kallisto
23    ```
24
251. Make a build directory and move there
26
27    ```
28    mkdir build
29    cd build
30    ```
31
321. Execute cmake. There are a few options:
33    - `-DCMAKE_INSTALL_PREFIX:PATH=$HOME` which will put kallisto in
34       `$HOME/bin` as opposed to the default (`/usr/local/bin`)
35
36    ```
37    cmake ..
38    ```
39
40    This is only required when one of the `CMakeLists.txt` files changes or new
41    source files are introduced. It will make a new set of `Makefile`s
42
431. Build the code
44
45    ```
46    make
47    ```
48
49    Optionally install into the cmake install prefix path:
50
51    ```
52    make install
53    ```
541. Run the code. The source tree hierarchy is copied, so you can find kallisto
55   at `src/kallisto` and tests at `test/tests`.
56
57After performing these steps, you can simply build using make as long as new
58source files aren't introduced or the `CMakeLists.txt` scripts aren't modified.
59