Installing from source

Although the kallisto and bustools binaries already come packaged within kb-python, perhaps the simple pip install isn't working for you and you wish to install kallisto and bustools separately.

Precompiled binaries

If you want to download the binaries separately, you can visit:

Compiling from source

If you want to install the kallisto and bustools software separately from source, you can do the following:

For kallisto:

git clone --branch v0.50.1 https://github.com/pachterlab/kallisto
cd kallisto
mkdir build
cmake ..
make
make install

For bustools:

git clone --branch v0.43.2 https://github.com/BUStools/bustools
cd kallisto
mkdir build
cmake ..
make
make install

If you want to install the latest version (not just specific versions), you can omit the --branch version specification from the above commands (e.g. omit --branch 0.43.2 when running git clone).

Tip

If you get permission denied errors from the make install step (e.g. because you don't have sudo privileges), you can simply use the local binaries. Those binaries will be located at kallisto/build/src/kallisto and bustools/build/src/bustools after compiling from source per the instructions above, and you can execute those binaries directly. Additionally, if you'd like, you can add those src directories to your path for easy access to running those binaries.

Warning

Installing kallisto from source in the manner above will not allow the production of h5ad files when doing bulk RNA-seq quantification. The h5ad files may be required for certain bulk RNA-seq differential gene expression programs. To enable generation of h5ad files, please modify the cmake command to be: cmake .. -DUSE_HDF5=ON

Note

By default, kallisto will only support k-mer lengths up to 31. In order to enable support for k-mer lengths up to 63 (which is optimal for long-read data), please modify the cmake command to cmake .. -DMAX_KMER_SIZE=64. Important: Always use a fresh installation (i.e. redownload the source code from github) when rerunning cmake because files that exist from a previous build may cause the binary to be generated incorrectly.

Using the binaries

You can also run the kb ref and kb count commands using your kallisto and bustools binaries downloaded separately or installed from source:

kb ref --kallisto=/path/to/kallisto --bustools=/path/to/bustools ...
kb count --kallisto=/path/to/kallisto --bustools=/path/to/bustools ...