Metadata-Version: 1.1
Name: dnasnout-client
Version: 0.2.0
Summary: DNASnout client
Home-page: http://www.cbs.dtu.dk/~laurent/dnasnout
Author: Laurent Gautier
Author-email: lgautier@gmail.com
License: This software is available under a dual license model: the AGPLv3 or a commercial license. If you need a commercial license, contact the author.
Description: About
        =====
        
        This script comes in support of the submitted paper:
        
        *Low-bandwidth and non-compute intensive remote
        identification of microbes from raw sequencing reads*.
        
        - It requires:
        
            - Python 3.3 (note the ".3")
        
            - bowtie2 (parameter "-a", try "--help")
        
        - It is self-documented (try "-h" or "--help").
        
        - It is working on FASTQ or gzipped-FASTQ files, possibly on BAM files
        
        Be gentle and please do not hammer the server like there is no tomorrow.
        
        The latest released versions of the package will always be on Pypi.
        
        Usage
        =====
        
        This installs as a regular Python package:
        
          python setup.py install
        
        Development version
        -------------------
        
           The following BASH lines show to install a development version in a virtual
           environment
        
           .. code:: bash
        
              # installation directory
              INSTALLDIR_CLIENT=./installclient_dir
        
              # install
              mkdir -p ${INSTALLDIR_CLIENT}
              # create a virtual environment (Python 3.3)
              # (if 3.3 is the only Python on your system, `pyvenv` will be enough)
              pyvenv-3.3 ${INSTALLDIR_CLIENT}/dnasnoutclient_env
        
              # use the virtual environment
              source ${INSTALLDIR_CLIENT}/dnasnoutclient_env/bin/activate
        
              # Install packages
              # bootstrap virtualenv
              wget https://bitbucket.org/pypa/setuptools/raw/bootstrap/ez_setup.py -O - | python
              # install pip
              easy_install pip
              # install dependencies
              #     numpy
              pip install numpy 
              #     bitarray
              pip install bitarray
              #     ngs_plumbing
              pip install https://bitbucket.org/lgautier/ngs_plumbing/get/default.tar.gz
              # install dnasnout-client
              pip install https://bitbucket.org/lgautier/dnasnout-client/get/default.tar.gz
              # installation is complete
              # deactivate the virtualenv
              deactivate
        
        
        Test the installation
        ^^^^^^^^^^^^^^^^^^^^^   
        
           .. code:: bash
        
              # use the virtual environment
              source ${INSTALLDIR_CLIENT}/dnasnoutclient_env/bin/activate
              cd ${INSTALLDIR_CLIENT}
              # download test data
              wget http://tapir.cbs.dtu.dk/static/iontorrent_head400.fq
              python -m dnasnout_client.console -i iontorrent_head400.fq -d iontorrent_test
        
        
        
        The module can be run directly:
        
          python -m dnasnout_client.console
        
        Help is available with:
        
          python -m dnasnout_client.console --help
        
        
        Oh, and here is a screenshot:
        
        .. image:: http://cbs.dtu.dk/~laurent/dnasnout/static/screenshot.png
           :alt: Screenshot
           :align: center
        
         
        
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
