How to install SortMeRNA tool on my university HPC cluster?
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2.0 years ago
Farah ▴ 70

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

RNA-Seq HPC Cluster cluster computing • 1.1k views
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2.0 years ago
AK ★ 2.0k

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.

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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

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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.

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That is great. Thank you so much.

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2.0 years ago
ATpoint 50k

I personally like to use the package manager Anaconda which allows local installation without root permission. See the documentation on how to install it. Once you have set it up, it is as easy as conda install -c biocore sortmerna.

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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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Thanks. By using Anaconda, can I install other software and tools as well? for example, Kallisto and STAR.

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Yes,basically everything and it takes full care of dependencies etc.

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Oh that is great. Thank you very much.

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