- Enter the following command to download the Trinity Assembly Kit:
wget https://sourceforge.net/projects/trinityrnaseq/files/Trinity-v/tar.gz
- Unzip the downloaded file:
tar -xzvf Trinity-v tar.gz
- Change into the unzipped directory:
cd Trinity-v
- In order to create a standalone Trinity executable, enter the following command:
make
- Trinity will now be installed in the current directory. You can test the installation by running Trinity like this:
./Trinity –help
trinity assembly
Ubuntu Trinity Desktop installieren
FAQ
How do I install Trinity assembler in Ubuntu?
There are a few ways to install Trinity in Ubuntu.
The first way is to download the Trinity package from Trinity’s website (http://trinityrnaseq.sourceforge.net). Once you have downloaded the Trinity package, you will need to unzip it. To unzip the package, open a terminal and navigate to the directory where you downloaded the package. Then, type the following command:
sudo unzip trinityrnaseq_r2013-02-25.zip
Once the package has been unzipped, you will need to navigate to the trinityrnaseq_r2013-02-25/trinity-plugins-1.6.0/BINARIES directory. To do this, type the following command:
cd trinityrnaseq_r2013-02-25/trinity-plugins-1.6.0/BINARIES
In the BINARIES directory, there should be a file called trinity- assembler. To install Trinity, you will need to type the following command:
sudo cp trinity-assembler /usr/local/bin/
The second way to install Trinity is through Bioconda (https://bioconda.github.io/). To install Trinity through Bioconda, you will first need to install Miniconda3 (https://docs.conda.io/en/latest/miniconda.html). Once you have installed Miniconda3, you will need to open a terminal and type the following command to install Trinity:
conda install -c bioconda trinity
The third way to install Trinity is through Docker (https://www.docker.com/). To install Trinity through Docker, you will first need to install Docker. Once you have installed Docker, you will need to pull the Trinity image from Docker Hub. To do this, type the following command:
docker pull trinityctat/trinity
Once the Trinity image has been pulled, you will need to run the Trinity container. To do this, type the following command:
docker run –rm -it -v /your/data/directory:/data trinityctat/trinity
What are the dependencies for Trinity assembler?
The Trinity assembler has a number of dependencies, most notably Perl and the GMP and MPFR libraries. Additionally, it requires the SAMtools, Bowtie, and R libraries be installed and configured properly.
Where can I find the Trinity assembler source code?
There is no definitive answer to this question as the Trinity assembler source code is not publicly available. However, there are a few potential sources that could be checked in an attempt to locate the source code:
1. The Trinity website (http://trinityassembly.org/) may have links to the source code, or at least instructions on how to obtain it.
2. There may be third-party websites that have mirrored the Trinity assembler source code. A web search using keywords such as “Trinity assembler source code” or “Trinity assembly source code” may turn up some results.
3. Some developers may have made their own modifications to the Trinity assembler source code and made it available online. A web search using keywords such as “Trinity assembler source code” or “Trinity assembly source code” followed by “modified” or “custom” may turn up some results.
4. It may be possible to find the Trinity assembler source code by decompiling the Trinity assembler executable. This is a more advanced approach and would require access to the Trinity assembler executable file.
How do I compile Trinity assembler from source?
First, you’ll need to download the Trinity source code. You can do this by cloning the Trinity GitHub repository.
Once you have the source code, you’ll need to compile it. To do this, you’ll need to have a C++ compiler installed on your system.
Once you have a C++ compiler installed, you can compile Trinity by running the following command from within the Trinity source code directory:
g++ -std=c++11 -o trinity trinity.cpp
This will produce an executable file called “trinity” that you can run to assemble your Trinity program.
Are there any known issues with Trinity assembler on Ubuntu?
Yes, there are several known issues with Trinity assembler on Ubuntu. Most notably, Trinity will not run on Ubuntu 12.04 and below due to incompatibilities with the glibc library. Additionally, Trinity may produce incorrect results on some versions of Ubuntu due to differences in how the Linux kernel handles memory. Finally, Trinity may not work correctly with certain versions of the Java Runtime Environment (JRE).