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sestaton / tephra

A tool for discovering transposable elements and describing patterns of genome evolution
MIT License
30 stars 3 forks source link

manual installation: missing modules for cpan in docs #31

Closed juancresc closed 6 years ago

juancresc commented 6 years ago

I've installed tephra manually, maybe I did something wrong or missed something, but i had to install many modules and libs for using it:

sudo apt-get install libmoosex-perl libpath-class-perl libgsl-dev libmoose-perl cpan Parallel::ForkManager cpan Bio::GFF3::LowLevel cpan YAML::Tiny cpan Bio::DB::HTS::Kseq cpan Log::Log4perl cpan App::Cmd cpan Path::Class cpan Log::Any cpan DateTime cpan Lingua::EN::Inflect cpan List::UtilsBy cpan Number::Range cpan Set::IntervalTree cpan Log::Any::Adapter::Log4perl

I've also had a hard time installing htslib. This is why I'd suggest to use the docker option (in our case it was not possible at the time)

sestaton commented 6 years ago

Hi,

There is no need to install anything manually in this fashion. As per the install docs, you can just type:

cpanm --installdeps .

And that will take care of the dependencies. Concerning HTSlib, you don't need to install this manually. When you run "perl Makefile.PL" this should be handled for you.

If you ran those commands, did you find that the installation was broken after you ran make test?

sestaton commented 6 years ago

I should note that a working C compiler and the program make are required to build from source, among some other core libraries. This may have been part of the issue.

juancresc commented 6 years ago

thank you for the clarification. I missed that command

sestaton commented 6 years ago

No worries, thank you for the response. I know there are quite a few dependencies but I've tried to make it as automated as possible.

Let me know if you have any further questions.