Hello,
For my RNA-seq analysis, I need to install SortMeRNA tool (for sudo alignment) on my university HPC cluster. As I am quite new in linux and cluster, I googled a lot, but I could not find how to do it. I would highly appreciate if you can help me in this regard.
Best wishes, Farah
Hi F. Golestan,
Did you find this manual?
You can download the pre-compiled code by: wget http://bioinfo.lifl.fr/RNA/sortmerna/code/sortmerna-2.1-linux-64-multithread.tar.gz,
and uncompress it using tar -zxvf sortmerna-2.1-linux-64-multithread.tar.gz.
The program: sortmerna-2.1b/sortmerna is already executable.
You can add the path in your script for HPC when using it, for example: export PATH="/home/user/src/sortmerna-2.1b":$PATH, which is where the uncompressed folder is.
Or, you can add export PATH="/home/user/src/sortmerna-2.1b":$PATH to ~/.bashrc directly, so that the executable indexdb_rna and sortmerna can be found in $PATH.
Hope it helps.
Thanks SMK. I could run the first two codes.
But, after running export PATH=$HOME/.local/bin:$PATH , then, I ran $ sortmerna and I got
-bash: sortmerna: command not found
Do I need to specify my path to the script? If so, how to find which path I should add and where is sortmerna located in my HPC path?
Also, as you mentioned, how to add export PATH="/home/user/src/sortmerna-2.1b":$PATH to ~/.bashrc directly?
Thank you very much.
Best wishes,
Farah
Hi F. Golestan,
Is $HOME/.local/bin where you uncompressed sortmerna-2.1-linux-64-multithread.tar.gz?
It has to be the path where the directory (sortmerna-2.1b) is.
how to add export PATH="/home/user/src/sortmerna-2.1b":$PATH to ~/.bashrc directly?
Check out To Set PATH on Linux.
Also there seems to a direct binary available http://bioinfo.lifl.fr/RNA/sortmerna/code/sortmerna-2.1-linux-64-multithread.tar.gz
I have not used it but I could extract and just a ./sortmerna seems to work.
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