Question: miRDeep2 installation 'make_html.pl'
0
gravatar for Barry Digby
6 months ago by
Barry Digby200
National University of Ireland, Galway
Barry Digby200 wrote:

Hi guys,

I have been following the installation steps for miRDeep2 outlined here: https://github.com/rajewsky-lab/mirdeep2. I am stuck on the final step of testing installation, testing the make_html.pl script. The error I receive is:

Can't locate PDF/API2.pm in @INC (@INC contains: PERL5LIB /home/bdigby/bin/mirdeep2/lib/perl5/site_perl/5.16.2 /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /home/bdigby/bin/mirdeep2/src/make_html.pl line 25.
BEGIN failed--compilation aborted at /home/bdigby/bin/mirdeep2/src/make_html.pl line 25.

I have tried to solve this by changing one of the @INC paths from "/home/bdigby/bin/mirdeep2/lib/perl5/site_perl/5.16.2" to "/home/bdigby/bin/mirdeep2/lib/PDF/" (where API2.pm is located), tried the two versions of perl on the cluster (and adjusted my @INC accordingly), to no avail. I am trying to test this installation on a cluster, running on Linux.

Any suggestions would be appreciated. I could try and ask the admin with root privelages to install PDF::API2 in the systems perl libraries for me, if it remedies this.

  • Barry
mirdeep2 pdf::api2 perl • 317 views
ADD COMMENTlink modified 6 months ago by RamRS24k • written 6 months ago by Barry Digby200
2
gravatar for RamRS
6 months ago by
RamRS24k
Houston, TX
RamRS24k wrote:

Perl errors of the format "Can't find XYZ/ABC.pm in @INC" can almost always be solved using cpan install XYZ::ABC, i.e. cpan install PDF::API2 in your case. I think going the sysadmin route is the way to go for now.

ADD COMMENTlink modified 6 months ago • written 6 months ago by RamRS24k
1

Thanks for the response, aforementioned sysadmin corrected it by adding

use lib '/home/bdigby/bin/mirdeep2/lib/';

to the header of the perl script and it worked :)

ADD REPLYlink written 6 months ago by Barry Digby200

Wonderful. So many ways to add a library location!

ADD REPLYlink written 6 months ago by RamRS24k
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