Installing spatula¶

Spatula contains htslib and qgenlib as submodules, so you need to clone the repository recursively to install the required libraries, and build the submodules before building the spatula package. An example instruction is given below.

## STEP 1 : CLONE THE REPOSITORY
## clone the current snapshot of this repository
git clone --recursive https://github.com/seqscope/spatula.git

## move to the spatula directory
cd spatula

## STEP 2 : BUILD THE SUBMODULES
## move to the submodules directory
cd submodules

## build the submodules using build.sh script
sh -x build.sh

## move to the spatula directory
cd ..

## STEP 3 : BUILD SPATULA
## create a build directory
mkdir build
cd build

## Run cmake to configure the build
cmake ..

## Build the spatula package
make

If cmake is not found, you need to install cmake in your system.

(Optional) Customized specification of the library path¶

In case any required libraries is missing in cmake, you may specify customized installing path by replacing "cmake .." with the following options:

## If qgenlib is missing or installed in a different directory
$ cmake -DQGEN_INCLUDE_DIRS=/qgenlib_absolute_path/include
        -DHTS_LIBRARIES=/qgenlib_absolute_path/lib/libqgen.a ..

## If htslib is missing or installed in a different directory
$ cmake -DHTS_INCLUDE_DIRS=/htslib_absolute_path/include/  \
        -DHTS_LIBRARIES=/htslib_absolute_path/libhts.a ..

## If bzip2 is missing or installed in a different directory
$ cmake -DBZIP2_INCLUDE_DIRS=/bzip2_absolute_path/include/ \
        -DBZIP2_LIBRARIES=/bzip2_absolute_path/lib/libbz2.a ..

## If lzma is missing or installed in a different directory
$ cmake -DLZMA_INCLUDE_DIRS=/lzma_absolute_path/include/ \
        -DLZMA_LIBRARIES=/lzma_absolute_path/lib/liblzma.a ..

## You may combine the multiples options above if needed.
## Other missing libraries can be handled in a similar way.

Testing spatula¶

To test whether build was successful, you can run the following command:

## Current directory: /path/to/install/spatula/build
$ ../bin/spatula --help