Create Trinity Dockerfile and version 2.11.0

Author: hlfernandez

trinity/2.11.0/Dockerfile

@@ -0,0 +1 @@
+FROM trinityrnaseq/trinityrnaseq:2.11.0 

trinity/README.md trinity/2.11.0/README.mdtrinity/README.md renamed to trinity/2.11.0/README.md

@@ -1,16 +1,16 @@
-#### Please, note that this repository does not contain any docker images. It just provides guidance on how to use the official Docker image. Read below for further information.
+#### 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](https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-in-Docker) explains how to use its docker image, which is available at the [trinityrnaseq/trinityrnaseq](https://hub.docker.com/r/trinityrnaseq/trinityrnaseq/tags/) repository. 
+The [Trinity wiki](https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-in-Docker) explains how to use its docker image, which is available at the [trinityrnaseq/trinityrnaseq](https://hub.docker.com/r/trinityrnaseq/trinityrnaseq/tags/) repository. The original Dockerfile is available [at GitHub](https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile).
 
-For instance, you can show the help by running `docker run --rm trinityrnaseq/trinityrnaseq Trinity -h`.
+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](http://cab.spbu.ru/software/spades/#examples): [left](http://spades.bioinf.spbau.ru/spades_test_datasets/ecoli_mc/s_6_1.fastq.gz) and [right](http://spades.bioinf.spbau.ru/spades_test_datasets/ecoli_mc/s_6_2.fastq.gz)
 
-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 trinityrnaseq/trinityrnaseq 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`
+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. 
@@ -23,4 +23,4 @@ Please note that the execution of this command may take a few hours, depending o
 
 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 trinityrnaseq/trinityrnaseq 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`
+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`