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EBI-Metagenomics / EukCC

Tool to estimate genome quality of microbial eukaryotes
GNU General Public License v3.0
35 stars 9 forks source link

Further guidance on GeneMark-ES installation #21

Closed mw55309 closed 3 years ago

mw55309 commented 3 years ago

Hey

Great tool!

It would be great if the documentation around installation of GeneMark-ES could be expanded.

For example, "apt" is not installed on our Linux cluster ;-)

Given the conda install, it would be good if some kind of recipe for using conda or pip could be implemented, including the ability to install non-system libraries (i.e. install perl libs into home directories)

Cheers Mick

openpaul commented 3 years ago

Hello,

apt is the package manager of Debian and Ubuntu, so please adapt to your linux setup ;-) All the documentation tells you to do, is to install perl correctly in order to run GeneMark-ES.

If you need help installing GeneMark-ES, you will need to look for help on their end (we do not provide GeneMark-ES, thats unrelated software).

Have a look around here: http://exon.gatech.edu/GeneMark

Sadly I could not make perl work only using conda on my end, thats why I suggest installation of cpanminus via apt. If you succeed, feel free to share and I will try to validate your approach.

I would love to have a complete Singularity Recipe for EukCC, but GeneMark-ES and Perl make it hard.

mw55309 commented 3 years ago

My very quick test shows this works to get GeneMark-ES running:

conda install perl-app-cpanminus

env PERL5LIB="" PERL_LOCAL_LIB_ROOT="" PERL_MM_OPT="" PERL_MB_OPT="" $CONDA_PREFIX/bin/cpanm inc::Module::Install::DSL Hash::Merge MCE::Mutex FindBin Test::Pod Logger::Simple  Parallel::ForkManager.pm YAML Math::Utils

Note1 you could add perl-app-cpanminus to the eukcc conda recipe

Note2 you're missing Math::Utils from your list of required Perl libs

openpaul commented 3 years ago

Thanks a lot. Math::Utils must have slipped through the cracks. Thank you for finding this.

I am currently building a container trying to verify that this works.