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EBI-Metagenomics / EukCC

Tool to estimate genome quality of microbial eukaryotes
GNU General Public License v3.0
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GeneMark-ES license #20

Open Lcornet opened 3 years ago

Lcornet commented 3 years ago

Dear all,

I would like to use EukCC, installed in a singularity (ubuntu), but I have an error with GeneMark-ES license

singularity exec --bind ${PWD}:/mnt eukcc.sif eukcc --db /mnt/eukccdb --ncores 4 --ncorespplacer 1 --outdir eukcc_testgenome /mnt/metabat/bin.19.fa 04/14/2021 15:33:11: Starting EukCC 04/14/2021 15:33:12: Running GeneMark-ES 04/14/2021 15:33:12: I could not find the license of GeneMark-ES. Make sure you have a valid license in your home directory with the name '.gm_key'. Will try to run GeneMark-ES regardless, but it will likely fail 04/14/2021 15:45:45: GeneMark-ES failed on this bin 04/14/2021 15:45:45: No estimates were written

The license key is the home (root) directory: singularity exec --bind ${PWD}:/mnt eukcc.sif ls /root/.gm_key /root/.gm_key

Di I need to place the license somewhere else ? This is how EukCC is installed :

eukcc

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
#eukcc via conda
conda install -y eukcc
cpanm inc::Module::Install::DSL Hash::Merge MCE::Mutex FindBin Test::Pod Logger::Simple  Parallel::ForkManager.pm YAML
#gmes
cd /opt/
tar -xzvf gmes_linux_64.tar.gz
cp -r gmes_linux_64/* /usr/local/bin/
zcat gm_key_64.gz > ~/.gm_key
openpaul commented 3 years ago

The license needs to be found by GeneMark, please have a look on http://exon.gatech.edu/GeneMark to find out exactly where to place the license.

In the versions I used it was always $HOME/.gm_key, but considering you are using singularity I am not sure where you would have to place the license exactly, as this depends on your mount paths.

For debugging I would suggest starting an interactive singularity shell.