Question: Help with miRDeep2 installation
0
gravatar for reswinvented
6.7 years ago by
reswinvented20
Canada
reswinvented20 wrote:

Doing a miRNA seq analysis. I don't know anything about command line scripts. I am trying to get started on the analysis by installing miRDeep2. Can't seem to get the install right because I am extremely confused with all the commands. From my understanding, with the miRDeep2 package, there is a file called install.pl that seems to have a script that will automatically install all the necessary files needed for the package. Can anyone give me some tutorial on how to start running this program and how I can at least install it? 

rna-seq • 5.0k views
ADD COMMENTlink modified 2.3 years ago by jlwebb20 • written 6.7 years ago by reswinvented20

It'll be helpful to know which operating system you're using.

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by Devon Ryan98k

Mac OSX Mavericks

ADD REPLYlink written 6.7 years ago by reswinvented20

Assuming you've extracted the zip file to Downloads, then:

cd ~/Downloads/mirdeep2
./install.pl
ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by Devon Ryan98k
1
gravatar for jlwebb
2.3 years ago by
jlwebb20
jlwebb20 wrote:

install mirdeep2 by visiting this website: https://github.com/rajewsky-lab/mirdeep2 download the zipped folder with everything and extract it to your desktop move into the folder from the command line and then type: turn on bash sudo perl install.pl source ~/.bash_profile perl install.pl

When this gives you an error for Font::TTF, run the following items: sudo apt-get install libfont-ttf-perl sudo apt-get install libpdf-api2-perl visit http://eddylab.org/software/squid/squid.tar.gz move into that folder using cd ./configure sudo make sudo make install

Then
isit http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.1.tar.gz cd into your randfold folder sudo make sudo mv randfold_folder_name_here /usr/local/bin/ alias randfold="/usr/local/bin/randfold/randfold"

cd back into your mirdeep2 folder Now run sudo perl install.pl again and see if that fixes your problems

ADD COMMENTlink written 2.3 years ago by jlwebb20
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