Metadata-Version: 1.2
Name: minFQ
Version: 1.4.0
Summary: Command line interface for uploading fastq files and monitoring minKNOW for minotour.
Home-page: https://github.com/LooseLab/minotourcli
Author: Matt Loose
Author-email: matt.loose@nottingham.ac.uk
License: MIT
Description: A client to upload reads to minoTour
        ====================================
        
        A command line client for uploading sequencing metrics from Oxford Nanopore Technologies MinKNOW to a LooseLab minoTour
        server instance.
        
        MinFQ only supports minknow core 4.X.X as it uses ONT's minknow-api, which is only compatible with said version of MinKNOW.
        
        However, base called data can be uploaded from any version of MinKNOW/Guppy.
        
        **To install -**
        
        .. code-block:: python
        
            pip install minFQ
        
        **Example Commands**
        
        In the example commands below example parameters are:
        
            - your_user_key: is the long string found in the profile section of your minoTour account.
        
            - url_to_your_minotour_server: Probably 127.0.0.1, could be a remote address like minotour.nottingham.ac.uk
        
            - port_for_your_server: Probably 8000
        
        To monitor both live and fastq data.
        
        .. code-block:: python
        
            minFQ -k [your_user_key] -w /path/to/your/fastq/files -ip 127.0.0.1 -hn
            [url_to_your_minotour_server] -p [port_for_your_server]
        
        To monitor just live data from minKNOW.
        
        .. code-block:: python
        
            minFQ -k [your_user_key] -ip 127.0.0.1 -hn [url_to_your_minotour_server]
            -p [port_for_your_server] -nf
        
        To monitor live data and enable limited remote control of minKNOW.
        
        .. code-block:: python
        
            minFQ -k [your_user_key] -ip 127.0.0.1 -hn [url_to_your_minotour_server]
            -p [port_for_your_server] -nf -rc
        
        To monitor just fastq data.
        
        .. code-block:: python
        
            minFQ -k [your_user_key] -w /path/to/your/fastq/files -hn [url_to_your_minotour_server]
            -p [port_for_your_server] -nm
        
        To monitor fastq statistics only. (Note you will not be able to run subsequent analysis on the server which requires sequence data).
        
        .. code-block:: python
        
            minFQ -k [your_user_key] -w /path/to/your/fastq/files -hn [url_to_your_minotour_server]
            -p [port_for_your_server] -nm -s
        
        To start an analysis remotely whilst uploading data. Note reference Id may not be required.
        
        .. code-block:: python
        
            minFQ -k [your_user_key] -w /path/to/your/fastq/files -hn [url_to_your_minotour_server]
             -p [port_for_your_server] -nm -j [job_id] -r [reference_id]
        
        **minFQ Gui**
        
        We are in the process of rebuilding a minFQ gui. Watch this space.
        
Keywords: nanopore quality control analysis
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.5
