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        "description": "[![Anaconda-Server Badge version](https://anaconda.org/w-l/deviate/badges/version.svg)](https://anaconda.org/w-l/deviate)\n[![Anaconda-Server Badge platforms](https://anaconda.org/w-l/deviate/badges/platforms.svg)](https://anaconda.org/w-l/deviate)\n[![Anaconda-Server Badge lastupdate](https://anaconda.org/w-l/deviate/badges/latest_release_date.svg)](https://anaconda.org/w-l/deviate)\n[![Anaconda-Server Badge downloads](https://anaconda.org/w-l/deviate/badges/downloads.svg)](https://anaconda.org/w-l/deviate)\n\n# deviaTE\n\ndeviaTE is a python tool for the analysis and visualization of mobile genetic element sequences. It is available for Unix and Linux systems.\n\n## Installation\n\n### Using Conda\n\nThe recommended way of using deviaTE is in a conda virtual environment. This way, all dependencies should be resolved.\n\nCreate a new conda virtual environment, and install deviaTE:\n\n```conda create deviaTE -c r -c defaults -c conda-forge -c bioconda -c w-l -n deviaTE_env```\n\nthis command loads all required anaconda channels (`r, defaults, conda-forge, bioconda, w-l`) and names the environment `deviaTE_env`\n\nThe environment can then be activated, and deviaTE with all necessary dependencies can be used inside the environment:\n\n```source activate deviaTE_env```\n\nAfter using deviaTE, the environment can be exited using:\n\n```source deactivate```\n\n\n### Using pip\n\nDeviaTE can also be installed with the pip python package manager. However, this does not take care of all dependencies. The following tools need to be set up manually beforehand:\n\n* python 3.6+\n* pip for python3 (https://pip.pypa.io/en/stable/installing/)\n* samtools (tested with version 1.6 and 1.9)\n* bwa (tested with version 0.7.17)\n* R (tested with version 3.4.3)\n  * required R packages are installed automatically upon first usage\n\nsamtools and bwa need to be in your `$PATH`\n\nDeviaTE can then be installed with \n\n```pip3 install deviaTE```\n\n\n## Uninstallation\n\nconda environment:\n\n```conda env remove -n deviaTE_env```\n\npip package:\n\n```pip3 uninstall deviaTE```\n\n\n## Usage manual and walkthroughs\n\nA manual and a walkthrough with examples using publicly available data can be found here:\n\n* [Manual](https://github.com/W-L/deviaTE/blob/master/doc/MANUAL.md) \n* [Walkthrough](https://github.com/W-L/deviaTE/blob/master/doc/WALKTHROUGH.md) \n\n\n## Bugs, issues, questions, suggestions ...\nIf you find any problems, have questions or ideas for further improvement please use the issue tracker on this repository, thanks!\n\n\n## License\ndeviaTE is licensed under the GPLv3 License\n\n\n\n",
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