Question: miRDeep2 technical problem
2
gravatar for alessandro.palma
2.0 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 mapper.pl 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 make_html.pl is: Can't locate PDF/API2.pm 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

Alex

rna-seq software error • 801 views
ADD COMMENTlink written 2.0 years ago by alessandro.palma30

Ciao Alessandro,

I have been able to install it using sudo cpan PDF::API2 and also then execute make_html.pl 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 make_html.pl as sudo perl make_html.pl?

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

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Kevin Blighe49k
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