Installing qgenlib¶

Directory structure¶

Before installing qgenlib, it is recommended to install htslib in the same directory you want to install qgenlib' (i.e.qgenlibandhtslib` should be siblings directories).

To visualize the directory structure of the installation, it should look like this:

/path/to/install
|-- htslib
|   `-- libhts.a
|-- qgenlib

Installing qgenlib¶

After installing htslib, you can clone the current snapshot of this repository to install as follows

## clone the current snapshot of this repository
$ git clone https://github.com/hyunminkang/qgenlib.git

## move to the qgenlib directory
$ cd qgenlib

## create a build directory
$ mkdir build

## move to the build directory
$ cd build

## run cmake to configure the build
$ cmake ..

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, you may specify customized installing path by replacing "cmake .." with the following options:

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

Building the library¶

Once cmake is run successfully without errors, you can build the library by typing:

## Current directory: /path/to/install/qgenlib/build
$ make

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

## Current directory: /path/to/install/qgenlib/build
$ ../bin/testqgen --tsv ../test/dummy.dat