Mirdeep2 Installation (Error In Make_Html.Pl)

Question

[liran0921]

Hi,

I am trying to install mirdeep2. At the last step, I tested make_html.pl and error appeared as following:

[liran@ip14-mp2 tools]$ make_html.pl Can't locate PDF/API2.pm in @INC (@INC contains: /home/liran/tools/mirdeep2/lib64/perl5 /home/liran/tools/ViennaRNA-2.1.2/install_dir/lib64/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/liran/tools/mirdeep2/make_html.pl line 9. BEGIN failed--compilation aborted at /home/liran/tools/mirdeep2/make_html.pl line 9.

Could anybody tell me what's wrong? And how to fix it?

Really need your help.

Thanks you!

[Simon Cockell]

it's probably quite likely the PDF::API2 module isn't installed on your system, cpan install PDF::API2 is probably the best/quickest way of fixing that. This module is listed in the README as a dependency.

[liran0921]

Thank you, Simon. I have installed the module. But I din't set the path correctly. Now it works.

[tikshyadav19]

I have installed cpan install PDF::API2

And still got error

Can't locate PDF/API2.pm in @INC (@INC contains: /home/nbri/Tikshana/Ath/small_RNA/mirDeep/mirdeep2/lib/perl5 /home/nbri/vaishali/TOMATO_SRNA/new_analysis/mirdeep2-master/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64
/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/nbri/Tikshana/Ath/small_RNA/mirDeep/mirdeep2/bin/make_html2.pl line 25.
BEGIN failed--compilation aborted at /home/nbri/Tikshana/Ath/small_RNA/mirDeep/mirdeep2/bin/make_html2.pl line 25

locate PDF/API2.pm

/home/nbri/.cpan/build/PDF-API2-2.041-0/blib/lib/PDF/API2.pm
/home/nbri/.cpan/build/PDF-API2-2.041-0/lib/PDF/API2.pm
/home/nbri/.cpan/build/PDF-API2-2.041-1/blib/lib/PDF/API2.pm
/home/nbri/.cpan/build/PDF-API2-2.041-1/lib/PDF/API2.pm
/home/nbri/.cpan/build/PDF-API2-2.041-2/blib/lib/PDF/API2.pm
/home/nbri/.cpan/build/PDF-API2-2.041-2/lib/PDF/API2.pm
/home/nbri/.cpan/build/PDF-API2-2.041-3/blib/lib/PDF/API2.pm
/home/nbri/.cpan/build/PDF-API2-2.041-3/lib/PDF/API2.pm
/home/nbri/anaconda3/lib/site_perl/5.26.2/PDF/API2.pm
/home/nbri/anaconda3/pkgs/perl-pdf-api2-2.035-pl526_0/lib/site_perl/5.26.2/PDF/API2.pm
/home/nbri/miniconda2/envs/metawrap-env/lib/site_perl/5.26.2/PDF/API2.pm
/home/nbri/miniconda2/pkgs/perl-pdf-api2-2.035-pl526_0/lib/site_perl/5.26.2/PDF/API2.pm

Answer 1

[cts]

It is trying to find a particular file "PDF/API2.pm" however it can't. Perl looks for .pm files in folders listed in the variable @INC. You can modify @INC in a number of ways. What you could do is find out where your file is located and add the folder to the PERL5LIB environmental variable in bash, that was it will always show up.

[liran0921]

Thanks. You are right. I have specified the path and it works now.

[tikshyadav19]

I tried export PERL5LIB=/home/nbri/anaconda3/lib/site_perl/5.26.2/PDF/API2.pm

still got same error