Metadata-Version: 2.1
Name: eukcc
Version: 0.0.1
Summary: Check eukaryotic genomes or MAGs for completeness and contamination
Home-page: UNKNOWN
Author: Paul Saary
Author-email: eukcc@paulsaary.de
License: UNKNOWN
Description: # EukCC
        
        Estimate completeness and contamination in Eukaryotes.
        
        **this software is under development and unstable. Updates might break or 
        enhance your experience**
        
        ## Install
        
        ### Dependencies
        
        **GeneMark-ES**
        
        If you want to predict genes install GeneMark-ES: http://exon.gatech.edu/GeneMark/license_download.cgi
        
        For this you need some perl libraries installed:
        
        ```
        cpan install YAML
        cpan install Logger::Simple
        cpan install Parallel::ForkManager.pm
        ```
        
        **HMMER**
        
        Just install HMMER from: http://hmmer.org/
        
        I used version 3.2.1 but any later version should work fine.
        
        
        **Pplacer**
        
        Install pplacer. I installed it via conda:
        
        ```
        conda install -c bioconda pplacer 
        ```
        
        I used version 1.1alpha19
        
        ### The package
        
        Get the database:
        
        ```
        
        ```
        
        ```
        git clone https://gitlab.ebi.ac.uk/saary/eukcc
        cd eukcc
        python3 setup.py sdist bdist_wheel
        pip3 install dist/eukcc-0.0.1.tar.gz
        ```
        
        ## Run it
        
        ```
        EukCC.py --help
        ```
        
        ### Example
        
        Run EukCC on a bunch of bins:
        
        ```
        EukCC.py -c config/dir outdir bins/*.fa
        ```
        
        
        
        ## FAQ
        
        **GeneMark-ES throws a lot of errors**
        Yes, id does. If it does not start at all try the 32 bit version 
        (with the 32 bit version licence). This worked for me.
        
        
        
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
