Installation

LoFreq comes bundled as two packages: (i) a source package or (ii) a binary/precompiled package. See below for specific instructions for each of the above listed options.

LoFreq is also available via Bioconda and Homebrew, which might be the most convenient installation option for most.

Prerequisites

From version 2.1.6 onwards LoFreq (lofreq call-parallel to be exact) requires bcftools to be installed.

Installation from Binary Packages

Download the binary LoFreq distribution matching your system (e.g. Linux or MacOSX) from the dist folder on Github and unpack it. LoFreq can then simply be called with ./lofreq_star-2.1.0/bin/lofreq (assuming you downloaded version 2.1.0). You can move the folder anywhere you like (just preserve its structure) or copy its contents to a system-wide installation path, e.g. /usr/local

cp -rv ./lofreq_star-2.1.0/* /usr/local/

After that you should be able to call LoFreq by simply typing lofreq (assuming /usr/local/bin/ is in your PATH which is the case on most systems).

Binary packages of versions before 2.1

Binary packages before 2.1 were installed differently: cd to the unpacked directory and use the following to install LoFreq (to /usr/local/):

bash binary_installer.sh 

If you don’t have admin rights or want to install LoFreq to a non-standard directory use the --prefix argument. e.g.

bash binary_installer.sh --prefix $HOME/local/

Then follow the instructions given below under Installation to a non-standard directory.

Installation from Source

To build the LoFreq source you will need

• a C compiler (e.g. gcc or clang)
• a Python 2.7 or Python 3 interpreter (2.6 won’t work for sure)
• zlib developer files
• HTSlib 1.4 or later

If those requirements are met, download LoFreq’s source package from the dist folder on Github, unpack it and cd to the newly created directory. Assuming you have admin rights, use the following to compile and install LoFreq:

./configure --with-htslib=/path-to-htslib 
make install

If you don’t have admin rights or want to install LoFreq to a non-standard directory use the --prefix argument. In that case you will also have to follow the instructions given below under Installation to a non-standard directory.

Note, you will need to give the absolute path to samtools and htslib, not a relative one!

Installation from Github

If you downloaded LoFreq’s source from Github (by cloning or downloading master as zip), you will need to do run ./bootstrap (once) before proceeding with the instructions above.

• If you get an error like this configure.ac:72: error: required file './ltmain.sh' not found, run libtoolize (or glibtoolize) first and then bootstrap again. After that you can proceed as described above with the GNU triplejump:

• configure
• make
• make install

Installation to a Non-Standard Directory

If you installed LoFreq to a non-system directory (e.g. your home-directory), you will have to make sure that the corresponding bin sub-directory is part of your PATH environment variable.

If you also want to use the non-essential Python tools that come with LoFreq, please also make sure to add the corresponding sub-directory to your PYTHONPATH.

For example, for the prefix setting mentioned above (i.e. $HOME/local/), you would need the following:

export PATH=$HOME/local/bin/
export PYTHONPATH=$HOME/local/lib/python2.7/site-packages/

The first line ensures that you can call LoFreq by simply typing lofreq. The second makes sure that the optionally installed Python tools work.

Further help

If the documentation above is not sufficient and you have trouble installing LoFreq, please ask for help on the mailing list or email us directly (see Contact).