General build steps:
- Prepare the build environment
- Get the sources from GitHub or from GitHub releases
- Build
SortmeRNA-4 is C++17 compliant, and requires a compiler that supports filesystem standard library.
Currently only GCC-9 and Windows SDK meet that requirement.
Ready to use GCC-9 distribution is only available on Debian (Ubuntu). It is not available on Centos, i.e. no Devtoolset-9 yet, and building GCC-9 on Centos is not trivial.
Clang has no support for the filesystem yet. LLVM 9.0 is due to be released later this year. At that time we'll get back to supporting builds with Clang on Linux and OSX.
The build is performed using a Python script provided with the Sortmerna distribution.
The script uses a configuration file env.yaml, which can be Optionally modified to customize the build.
This is for Debian distros (Ubuntu)
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt update
sudo apt -y install gcc-9 g++-9
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-9
sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-9 9
sudo update-alternatives --install /usr/bin/cpp cpp-bin /usr/bin/cpp-9 60
# select gcc-9
sudo update-alternatives --config gcc
# select cpp-9
sudo update-alternatives --config cpp-bin
gcc --version
gcc (Ubuntu 9.2.1-17ubuntu1~16.04) 9.2.1 20191102
TODO.
This section is for RHEL (Centos) distros. Waiting for Devtoolset-9 to become available.
The sources can be placed in any directory, but here we use the user's Home directory
# clone the repository
git clone https://github.com/biocore/sortmerna.git
# alternatively get the release sources
wget https://github.com/biocore/sortmerna/archive/v4.0.0.tar.gz
tar xzf v4.0.0.tar.gz
pushd sortmerna
# If you need a particular release (tag)
git checkout v4.0.0
Use the build.py python script provided with Sortmerna distro.
The following installs Conda, and the python packages pyyaml, and jinja2 in the User's Home directory.
SMR_HOME=$HOME/sortmerna
python $SMR_HOME/scripts/build.py --name cmake
ls -lrt
drwxrwxr-x 15 biocodz biocodz 4096 Nov 18 09:43 miniconda3
# add Conda binaries to the PATH
export PATH=$HOME/miniconda3/bin:$PATH
The following installs CMake in user's home directory
SMR_HOME=$HOME/sortmerna
python $SMR_HOME/scripts/build.py --name cmake
[cmake_install] Installed CMake /home/biocodz/cmake-3.15.5-Linux-x86_64/bin/cmake
# add cmake to PATH
export PATH=$HOME/cmake-3.15.5-Linux-x86_64/bin:$PATH
All required third party libraries will be checked and installed automatically (in User directory by default) The default build won't interfere with any existing system installation.
By default the build produces statically linked executable i.e. portable.
SMR_HOME=$HOME/sortmerna
# modify configuration (optional)
vi $SMR_HOME/scripts/env.yaml
# run the build
python $SMR_HOME/scripts/build.py --name all [--env $SMR_HOME/script/my_env.yaml]
Download and Install VS Community edition from Visual Studio community website
Installer for Windows can be found here
TODO
TODO
TODO
Various features in SortMeRNA are dependent on third-party libraries, including: