This is ongoing development of SortMeRNA. For the latest stable release, see http://bioinfo.lifl.fr/RNA/sortmerna/.

WARNING: Do not attempt to run _autotools_batch_.sh unless you have Autotools installed. This script is for producing a distribution version of the code.

NOTE: the Clang compiler on Mac (distributed through Xcode) does not support multithreading. A preliminary implementation of OpenMP for Clang has been made at "http://clang-omp.github.io" though has not been yet incorporated into the Clang mainline. The user may follow the steps outlined in the above link to install the version of Clang with multithreading support, though this version has not yet been tested with SortMeRNA. Otherwise, the user is recommended to install the original GCC compiler via MacPorts (contains full multithreading support).

(1) Check your GCC compiler is version 4.0 or higher:

gcc --version

(2) Run configure and make scripts:

bash ./build.sh

Note: make install is not called in this script. However, any arguments given to build.sh will be passed to the configure script. If you plan on calling make install afterwards, then you can set your installation directory using build.sh --prefix=/path/to/installation/dir. Otherwise, you can simply copy the binaries sortmerna and indexdb_rna to your installation directory after calling build.sh.

(1) Check the version of your C/C++ compiler:

gcc --version

If the compiler is LLVM-GCC (deprecated, see Deprecation and Removal Notice), then you must set it to Clang or the original GCC compiler (installable via MacPorts).

(2a) To set your compiler to Clang (check you have it "clang --version", if not then see "Install Clang for Mac OS" below):

export CC=clang
export CXX=clang++

(2b) To set your compiler to the original GCC (check you have it "gcc-mp-4.8 --version", if not then see "Install GCC through MacPorts" below. Note the GCC compiler comes in many versions, 4.8 is one of the latest):

export CC=gcc-mp-4.8
export CXX=g++-mp-4.8

(3) Run configure and make scripts:

bash ./build.sh

Note: make install is not called in this script. However, any arguments given to build.sh will be passed to the configure script. If you plan on calling make install afterwards, then you can set your installation directory using build.sh --prefix=/path/to/installation/dir. Otherwise, you can simply copy the binaries sortmerna and indexdb_rna to your installation directory after calling build.sh.

Installing Xcode (free through the App Store) and Xcode command line tools will automatically install the latest version of Clang supported with Xcode.

After installing Xcode, the Xcode command line tools may be installed via:

Xcode -> Preferences -> Downloads

Under "Components", click to install "Command Line Tools"

Assuming you have MacPorts installed, type:

sudo port selfupdate
sudo port install gcc48

After the installation, you should find the compiler installed in /opt/local/bin/gcc-mp-4.8 and /opt/local/bin/g++-mp-4.8 .

If you use SortMeRNA, please cite: Kopylova E., Noé L. and Touzet H., "SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data", Bioinformatics (2012), doi: 10.1093/bioinformatics/bts611.