Question: (Closed) miRDeep2 technical problem
gravatar for alessandro.palma
2.8 years ago by
alessandro.palma30 wrote:

Hi all! I am trying to use miRDeep2 to analyze some miRNA-seq data, but I am facing off some technical problems. Actually I could install and run some of the scripts, such as and others, but I am having problems with installing the PDF::API2 perl module(which is needed to run some scripts and browsing results). I have been looking on the internet, in order to see if someone else could have had the same problem and how they fixed it, but I couldn't find the right answer. It's seems like my system doesn't recognize the PDF::API2 module even though I followed all the instructions provided within the software documentation. The error I got when I type is: Can't locate PDF/ in @INC (you may need to install the PDF::API2 module)... I tried to install it by the source code, with cpan PDF:API2, with sudo cpan PDF::API2 or everything else I found on internet (also tried both the latest version of the module, and the version of the mirDeep2 documentation). I obviously added the library to the PERL5LIB and restarded my shell, but it looks like that's not the problem... Furthermore, when I run the make command I got no repsonse, with make test I got a lot of warnings and tests failed, and finally with make install it doesn't install anything...tried everything as user and root. Could someone help me please? Thanks


rna-seq software error • 1.1k views
ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 2.8 years ago by alessandro.palma30

Ciao Alessandro,

I have been able to install it using sudo cpan PDF::API2 and also then execute successfully on my system (Ubuntu 14.04). My Perl libraries are stored in /home/kblighe/perl5/

Are the access rights to the perl module set to root by any chance? What if you run as sudo perl

This same issue was reported previously: Mirdeep2 Installation (Error In Make_Html.Pl)

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Kevin Blighe63k

Hello alessandro.palma!

We believe that this post does not fit the main topic of this site.

Closed since OP never followed up.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.


ADD REPLYlink written 5 months ago by ATpoint36k
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