The non-plotting programs in cellbouncer require only HTSLib and zlib. If you want to be cocky about it, you can just install those two dependencies and then clone and compile this repository:
git clone --recurse-submodules git@github.com:nkschaefer/cellbouncer.git
cd cellbouncer
make
You will not be able to run the plotting scripts unless you also install all needed R packages.
conda is a useful package manager that can be used to install CellBouncer dependencies. We also recommend installing mamba, which is an add-on for conda that is able to locate packages more quickly.
We provide several configuration files that can be used to create conda environments for use with CellBouncer. The file cellbouncer_minimum.yml contains all dependencies you need to run cellbouncer programs and make plots. The file cellbouncer_extra.yml also includes other programs useful for processing/analyzing data outside of cellbouncer that are mentioned in these help pages.
Note for Mac users: The file cellbouncer_extra_osx.yml is a version of cellbouncer_extra.yml that omits the program FastK, which is not available through conda for Mac OSX. If you want to use that program on a Mac, you will need to install it through other means. Additionally, M1 Macs can run programs compiled for both x86_64 and arm64 architectures (and conda doesn't care which by default), but attempting to link against programs compiled for one architecture while compiling for the other will cause problems. Therefore, you need to set a special variable before creating the conda environment if using an M1 Mac (see below).
Installing a conda environment
(CONDA_SUBDIR=osx-arm64) [conda/mamba] env create --file=[cellbouncer_minimum/cellbouncer_extra/cellbouncer_extra_osx].yml
conda activate cellbouncer
The first part (CONDA_SUBDIR=osx-arm64) should only be included if you are installing on a silicon M1+ Mac.
The environment you choose should either be cellbouncer_minimum.yml if you only want necessary dependencies, cellbouncer_extra.yml if you want to include extra programs, or cellbouncer_extra_osx.yml if you want to include extra programs and are on a Mac.
The only thing you need to do to compile is run make, and all compiled programs will be in the root-level directory. In the root (cellbouncer) directory:
make
or, if you have compiled old code and are updating:
make clean
make
If you have installed a conda environment, be sure to run conda activate cellbouncer to activate the environment before you run any CellBouncer programs.
CellBouncer depends on several other repositories included as git submodules. If you forget the --recurse-submodules option in your git pull command above, you can get all the submodules with
git submodule update --init --recursive
If you later need to update a local CellBouncer to the latest version, you can do so like this:
git pull --recurse-submodules
git submodule update --remote
make clean
make