Note : Building from the Github repository additionally requires invoking autoreconf --install to generate the configure script. autoreconf can be installed on Ubuntu using sudo apt-get install autoconf automake.
Clone the git repository.
git clone https://github.com/hasindu2008/f5c && cd f5c
Alternatively, download the latest release tarball and extract. eg :
VERSION=v1.4
wget "https://github.com/hasindu2008/f5c/releases/download/$VERSION/f5c-$VERSION-release.tar.gz" && tar xvf f5c-$VERSION-release.tar.gz && cd f5c-$VERSION/
While we have tried hard to avoid the dependency hell, three dependencies (zlib, HDF5 and HTS) could not be avoided.
Currently 3 building methods are supported.
- Locally compiled HTS library and system wide HDF5 library (recommended)
- Locally compiled HTS and HDF5 libraries (HDF5 local compilation - takes a bit of time)
- System wide HTS and HDF5 libraries (not recommended as HTS versions can be old)
Method 1 (recommended)
Dependencies : Install the HDF5 (and zlib development libraries)
On Debian/Ubuntu : sudo apt-get install libhdf5-dev zlib1g-dev
On Fedora/CentOS : sudo dnf/yum install hdf5-devel zlib-devel
On Arch Linux: sudo pacman -S hdf5
On OS X : brew install hdf5
Now build f5c
autoreconf # skip if compiling a release, only required when building from github
scripts/install-hts.sh # download and compiles htslib in the current folder
./configure
make # or make cuda=1 if compiling for CUDA
Method 2 (time consuming)
Dependencies : Install the zlib development libraries
On Debian/Ubuntu : sudo apt-get install zlib1g-dev
On Fedora/CentOS : sudo dnf/yum install zlib-devel
Now build f5c
autoreconf # skip if compiling a release, only required when building from github
scripts/install-hts.sh # download and compiles htslib in the current folder
scripts/install-hdf5.sh # download and compiles HDF5 in the current folder
./configure --enable-localhdf5
make # or make cuda=1 if compiling for CUDA
Method 3 (not recommended)
Dependencies : Install HDF5 and hts
On Debian/Ubuntu : sudo apt-get install libhdf5-dev zlib1g-dev libhts1
Now build f5c
autoreconf # skip if compiling a release, only required when building from github
./configure --enable-systemhts
make # or make cuda=1 if compiling for CUDA