pegi3s/trinity repository overview

⁠Please, note that this repository only contains a mirror to the trinityrnaseq/trinityrnaseq Docker image, providing guidance on how to use it. This way, we can keep a copy of this Docker image in our account for the sake of repeatability. Read below for further information.

⁠Trinity

The Trinity wiki⁠ explains how to use its docker image, which is available at the trinityrnaseq/trinityrnaseq⁠ repository. The original Dockerfile is available at GitHub⁠.

For instance, you can show the help by running docker run --rm pegi3s/trinity Trinity -h.

⁠Using the Trinity image in Linux

To test the Trinity docker image you can download these two E. coli FASTQ files from the SPAdes examples⁠: left⁠ and right⁠

For instance, to perform a basic assembly of RNA-Seq data you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/trinity Trinity --seqType fq --left /data/s_6_1.fastq.gz --right /data/s_6_2.fastq.gz --CPU 4 --max_memory 8G --output /data/trinity_results

Results will be generated in your/data/dir/trinity_results. In this command, you just need to replace:

• /your/data/dir to point to the directory that contains the FASTQ file you want to analyze.
• --CPU 4 to set a number of cores appropiate to your hardware configuration.
• --max_memory 8G to set an amount of RAM memory appropiate to your hardware configuration.

Please note that the execution of this command may take a few hours, depending on the hardware settings.

⁠Using the Trinity image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

You should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/trinity Trinity --seqType fq --left /data/s_6_1.fastq.gz --right /data/s_6_2.fastq.gz --CPU 4 --max_memory 8G --output /data/trinity_results