Installing Trinity
Note: The procedure is adapted from GitHub. All commands to be entered into the terminal are marked in gray.
Downloading the latest Trinity software to a Linux server, then simply type
make
in the base installation directory. This should build Inchworm and Chrysalis, both written in C++. Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software, but Java-1.8 (or higher) is required.
Installing Java
sudo apt-get update && apt-get upgrade # Updates Ubuntu linux
sudo apt-get install default-jdk # Installs default JDK
java –version # to check java version
Note: Trinity-v2.8 and onward, cmake is required for building the software.
C++ compiler (supporting C++11) and “make” must first be installed.
sudo apt update # updates the repositories
sudo apt install build-essential # installs essential packages
Run the “bootstrap” script you find in the source directory of CMake. You can use the “--help” option to see the supported options. You may use the “--prefix=<install_prefix>“ option to specify a custom installation directory for CMake. You can run the “bootstrap” script from within the CMake source directory or any other build directory of your choice. Once this has finished successfully, run “make” and “make install”. In summary execute the following commands.
sudo wget https://cmake.org/files/v3.4/cmake-3.4.1-Linux-x86_64.tar.gz
# downloads the cmake package
tar xf cmake-3.4.1-Linux-x86_64.tar.gz # extracts the archive
cd cmake-3.4.1-Linux-x86_64 # move in to the extracted directory
./bootstrap && make && make install # running bootstrap, make and install
export PATH="`pwd`/cmake-3.4.1-Linux-x86_64/bin:$PATH" # setting path
# save it in ~/.bashrc if needed
which cmake # will tell where cmake is installed
If you want to install Trinity in a central location (not required), you can make install and it'll copy the software package to /usr/local/bin/trinityrnaseq-version. You can set the environmental variable TRINITY_HOME to point to the above location, which will make it easy to access both Trinity as well as supported downstream applications that come bundled with Trinity.
export TRINITY_HOME=”path to trinity installation directory”
You can put the above command in your ~/.bashrc file so it'll be available to you by default.
Afterwards, you may want to build the additional plugin components that provide support for downstream analyses in which case you would then type:
make plugins
Additional tools required for running Trinity include:
Installing bowtie2
sudo wget --no-check-certificate https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.3/bowtie2-2.3.4.3-source.zip
sudo unzip bowtie2-2.3.4.3-source.zip
cd bowtie2-2.3.4.3
sudo make && sudo make install
Installing jellyfish
sudo wget –no-check-certificate
https://github.com/gmarcais/Jellyfish/releases/download/v2.2.10/jellyfish-2.2.10.tar.gz
tar -xvzf jellyfish-2.2.10.tar.gz
cd jellyfish-2.2.10
./configure
sudo make && sudo make install
salmon (Trinity can work without salmon but the run will be considerably slow)
Salmon Needs Boost C++ libraries
Installing Boost
Method 1
sudo wget –no-check-certificate https://dl.bintray.com/boostorg/release/1.68.0/source/boost_1_69_0.zip
sudo unzip boost_1_69_0.zip
cd boost_1_69_0
sudo ./bootstrap.sh
sudo ./b2 install
Set PATH to bin of Boost installation
Method 2
sudo apt-get install libboost-all-dev
Salmon also needs Threading Building Blocks (TBB)
Installing Threading Building Blocks
sudo apt-get install libtbb-dev
Installing Salmon
sudo wget --no-check-certificate https://github.com/COMBINE-lab/salmon/archive/v0.12.0-alpha.tar.gz
mv v0.12.0-alpha.tar.gz Salmon0.12.0-alpha.tar.gz
tar -xvzf Salmon0.12.0-alpha.tar.gz
cd Salmon0.12.0-alpha
cmake -DBOOST_ROOT=/Home_DIR_of_boost_1_69_0_installed_earlier/
sudo make
sudo make install