miRDeep2.0.0.8 install error occured

Question

[Yamiru]

Hi i just install miRDeep2 on my ubuntu.

and following guide... i typed this command on my linux

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cd mirdeep2_0_0_8

./install.pl

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but I got this message

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gcc version: 4.8.4-2ubuntu1~14.04.1) already installed, nothing to do ...

bowtie already installed, nothing to do ...

RNAfold 2.2.5

blahblahblahblahblahblahblahblahblahblahblahblahblahblahblahblahblah ..........................................................................................................................................................

randfold already installed, nothing to do ...

Compress::Zlib already installed, nothing to do ...

Font::TTf already installed, nothing to do ...

PDF::API2 already installed, nothing to do ...

RNAfold was/is not installed properly

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and i change directory into ./bin and typed ./maaper.pl, then this statement came out

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Please run the install.pl script first before using the miRDeep2 package

The install script is located in /TOOLS/mirdeep2_0_0_8/ so just do

cd /TOOLS/mirdeep2_0_0_8/

perl install.pl

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how can i do it?

Answer 1

[A. Domingues]

As fas as can tell the external package RNAfold is needed by mirDeep2 but is not available in your system. From my own instalation notes here is how to install it, but before doing it, read the RNAfold installation instructions .

ViennaRNA Package

This installs the latest RNAfoldq program which is required by miRDeep2.

cd ~/bin # change path to whichever folder you want to install it to
wget 'http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.9.tar.gz' 
tar -xzfv ViennaRNA-2.1.9.tar.gz
cd ViennaRNA-2.1.9/ 

# I wanted to have it installed in a particular folder - make install should be enough and you can ignore ./configure
# ./configure --prefix=/home/adomingu/imb-kettinggr/common_bin/ViennaRNA/2.1.9/ViennaRNA/
make install  

[Yamiru]

Yes I already installed that ViennaRNA package like you did and I set the Path of ViennaRNA on bashrc file. So when I type RNAfold then terminal said

Input string (upper or lower case); @ to quit
...,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8

but mirdeep2 still has problem...

[A. Domingues]

mirdeep2 still has problem

is it the same problem as described in your first post or a new one? We can't help without details.

[Yamiru]

Also I just solved it by type this on miRDeep folder

touch install_successful

and tested by using tutorial_dir/run_tut.sh

It works all right... but I dont know why it works;;

maybe I think installed all dependancies before install mirdeep2, so it works well..

[justa.dk]

And since then (after this touch install_successful) mirdeep works? How was the performance on your dataset?

[opplatek]

Thanks, this worked for me. I installed all dependencies and then ran perl install.pl in mirdeep2 folder. It gave me an error during ViennaRNA installation. I checked created bin directory in mirdeep2 folder and I saw a soft-link for RNAfold package pointing to "newly" installed RNAfold by install.pl. I replaced this soft-link with my installation of RNAfold and then I did the touch install_successful and it looks it's working. I guess it would work without changing the soft-link but I did it anyway just to be sure it points to the correct installation of RNAfold installed by me and not by install.pl. But as you said - I am not sure why it works but it does.

[Yamiru]

Oh sorry. It's same. but, what I want to say is "why RNAfold got a problem during installation??". because before download mirdeep2, I already downloaded all dependency, ofcourcely include ViennaRNA tool which contains RNAfold binary file. And I made double check that all dependency work or not. --> works well. (I want show you that RNAfold works well).

Answer 2

[aj03]

Hi, I am having the same problem as discussed above. Any Solution for this???

perl install.pl

. . . .

randfold already installed, nothing to do ...

Compress::Zlib already installed, nothing to do ...

Font::TTf already installed, nothing to do ...

PDF::API2 already installed, nothing to do ...

RNAfold was/is not installed properly

when i am running tutorial_dir/run_tut.sh its working properly but when i am running mirdeep2.pl its throwing error (RNAfold eror)

report.log:

computing randfold p-values select_for_randfold.pl mirdeep_runs/run_17_11_2016_t_14_17_29/tmp/signature.arf mirdeep_runs/run_17_11_2016_t_14_17_29/tmp/precursors.str > mirdeep_runs/run_17_11_2016_t_14_17_29/tmp/precursors_for_randfold.ids

started: 14:19:59

Use of uninitialized value $lng in numeric le (<=) at /opt/mirdeep2_0_0_8/src/select_for_randfold.pl line 266, <filename> line 118.

Use of uninitialized value in numeric le (<=) at /opt/mirdeep2_0_0_8/src/select_for_randfold.pl line 686, <filename> line 118.

Use of uninitialized value in numeric le (<=) at /opt/mirdeep2_0_0_8/src/select_for_randfold.pl line 714, <filename> line 118.

Use of uninitialized value in numeric le (<=) at /opt/mirdeep2_0_0_8/src/select_for_randfold.pl line 686, <filename> line 118.

. . .

error.log:

RNAfold: invalid option -- n