Perl modules for RepeatModeler

Question

[kirillkirilenko]

I am trying to install Perl modules for RepeatModeler. I am using conda Perl, most of the required modules I installed just via conda (bioconda), but some I couldn't. So, I read many Perl modules distribute through cpan, I installed cpan and some of the left modules I could install via cpan with command for example cpanm URL.

But I still can not install two modules: Devel::Size and LWP::UserAgent. For example when I execute cpan --force Devel::Size it returned (in a log file): /tmp/build/80754af9/perl_1527832170752/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc: not found

As written here I need x86_64-conda_cos6-linux-gnu-c++. But I already have it

Could anyone help me to handle it? Either install it via conda or another way. Thanks!

Answer 1

[Juke34]

To install perl-devel via conda: conda install -c bioconda perl-devel-size

The RepeatModeler recipe in bioconda is fixed since 1/2 years. Before it was an empty shell indeed...

To install RepeatModeler (perl-devel is installed with) via conda:

conda install -c bioconda repeatmodeler

Tools installed with repeatmodeler via bioconda:
alignAndCallConsensus.pl generateSeedAlignments.pl viewMSA.pl Linup

note that not all utils are linked directly in bin/, but
can still be accessed via ${PREFIX}/share/RepeatModeler/util/*.pl

[Michael]

Thanks for checking up on the conda recipe!

Answer 2

[Michael]

RepeatModeler should not require Devel::Size (see: https://github.com/Dfam-consortium/RepeatModeler/issues/154 ). I cannot build this module either on my system due to a make error, but it should not be needed. If the error persists, find the line in the RepeatModeler code saying use Devel::Size and remove it.

Note: You seemingly have CentOS 6 ("cos6"), you will run all sorts of problems with bioinformatics software over time. CentOS 6 is unsupported and you should upgrade your system to either CentOS 7 or a different distribution.