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.
Thanks for the response, aforementioned sysadmin corrected it by adding
to the header of the perl script and it worked :)
Wonderful. So many ways to add a library location!