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miRDeep2

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miRDeep2

miRDeep2 writes data to the mIRDeep2 installation directory. For this reason, we cannot install miRDeep2 on Artemis in the usual location (/usr/local). Instead, you can install miRDeep2 in your own /home, /project, or /scratch directories. The below commands will install miRDeep2 into a directory called /project/PANDORA/miRDeep2. It includes a hack of the make_html.pl and make_html2.pl files such that they run using the perl in the perl/5.28.0 module instead of /usr/bin/perl.


mIRDeep2 Artemis installation
cd /project/PANDORA
module purge
module load git
module load perl/5.28.0
module load gcc/7.2.0
git clone https://github.com/rajewsky-lab/mirdeep2.git
cd mirdeep2
git checkout tags/v0.1.0
perl install.pl
source ~/.bash_profile
perl install.pl
sed -i '1 s_#!/usr/bin/perl_#!/usr/bin/env perl_' bin/make_html.pl
sed -i '1 s_#!/usr/bin/perl_#!/usr/bin/env perl_' bin/make_html2.pl

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