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README.md

Installation

Requirements

Compilation: C++14 compliant compiler with OpenMP support, and CMake v3.1 or newer.

Compiling

Enter the Themisto directory and run

cd build
cmake ..
make

This will produce the build_index, pseudoalignment, and themisto_tests executables in the build/bin/ directory.

(Optional) Check if everything compiled correctly by running tests:

bin/themisto_tests

If there is a problem, the tests will terminate and report an error message.

If you run into problems involving zlib or bzip2, you can instruct the build process to download & compile them from source with

cmake -DCMAKE_BUILD_ZLIB=1 -DCMAKE_BUILD_BZIP2=1 ..
make

Compiling on macOS

Compiling Themisto on macOS requires users to first install gcc-6.1 or newer from homebrew with

brew install gcc@6

Afterwards, Themisto can be compiled by entering the directory and running

cd build
cmake -DCMAKE_C_COMPILER=$(which gcc-6) -DCMAKE_CXX_COMPILER=$(which g++-6) ..
make

Note that macOS has a very small limit for the number of concurrently opened files. Themisto can use temporary files to conserve RAM, and may run into this limit. To increase the limit, run the command

ulimit -n 2048

Usage

Indexing

To build the index, run:

build_index

The program will then print instructions on how to use it.

Pseudoalignment

To pseudoalign against the index, run:

pseudoalign

The program will then print instructions on how to use it.

License

This software is licensed under GPLv2. See LICENSE.txt.

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