Metadata-Version: 1.0
Name: KrATER
Version: 0.25
Summary: UNKNOWN
Home-page: https://github.com/mahajrod/KRATER
Author: Sergei F. Kliver
Author-email: mahajrod@gmail.com
License: UNKNOWN
Description: # KrATER (K-mer Analysis Tool Easy to Run)
        
        I. Requirements
        
            1. Python libraries:
                Matplotlib
                Numpy
                Scipy
                
            2. Jellyfish 2
        
        II. Installation
        
            1. Install requirements 
                - install jellyfish 2.x.x  from http://www.genome.umd.edu/jellyfish.html
            
                - install python libraries(not necessary if you going to install KrATER via pip)
                    - run following command for global installation
                
                        sudo pip install matplotlib numpy scipy 
                    
                    - or following command for local installation if you don't have root permissions
                
                        pip install --user matplotlib numpy scipy
                    
            2. Install KrATER
                Variant 1: install using pip
                
                   - run following command for global installation
                   
                        sudo pip install krater
                   
                   - run following commands for local installation
                        
                        pip install --user krater
                        
                      Then add ~/.local/bin in your PATH variable
                      
                        cat "PATH=\${PATH}:~/.local/bin/" >> ~/.profile
                        cat "PATH=\${PATH}:~/.local/bin/" >> ~/.bashrc
                        
                      Load updated PATH variable
                      
                        source ~/.profile
                    
                Variant 2: install from source code with root permissions
                
                    git clone https://github.com/mahajrod/krater
                    cd krater
                    python setup.py build
                    sudo python setup.py install
                
                
                Variant 3: install from source code without root permissions
                
                    Get KRATER
                        git clone https://github.com/mahajrod/krater
                
                    Add following strings to ~/.profile and ~/.bashrc (create files if absent). Don't forget to replace <KRATER_DIR> with actual path
                    
                        PYTHONPATH=${PYTHONPATH}:<KRATER_DIR>
                        PATH=${PATH}:<KRATER_DIR>
                        export PYTHONPATH
                        export PATH
                        
                    Run in terminal
                        source ~/.profile
                    
            
        III. RUN
        
            1. If input file/files is/are fastq:
            
                Typical usage:
                    draw_kmer_distribution_from_fastq.py -m 23  -t ${THREAD_NUMBER} -b -s 30G -e png -o ${OUTPUT_PREFIX} -i {COMMA_SEPARATED_LIST_OF_FASTQ_FILES} -w ${MINIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE}  -g ${MAXIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE}
                
                Parameter description:
                
            2. If input file is jellyfish database
                
                Typical usage:
                    draw_kmer_distribution_from_jellyfish_database.py -i ${JELLYFISH_DATABASE}  -o ${OUTPUT_PREFIX} -w ${MINIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE} -g ${MAXIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE} -e png
                
            2. If input file is histogram file produced by Jellyfish:
            
                Typical usage
                    draw_kmer_distribution_from_histo.py  -i ${JELLYFISH_HISTO_FILE}  -o ${OUTPUT_PREFIX} -w ${MINIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE} -g ${MAXIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE} -e png
                
                Parameter_description:
                
Platform: UNKNOWN
