CNV Analysis

CNV analysis is for: XXXX

Config

[CNV]
bowtie2 = /mnt/gpfs/Database/softs/anaconda2/bin/bowtie2
samtools = /mnt/gpfs/Database/softs/anaconda2/bin/samtools

[CNV_ref_hg19]
bowtie2_index = /mnt/gpfs/Database/ref/hg19/hg19
dynamic_bin = /mnt/gpfs/Users/zhangxiannian/basematic/cnv/hg19.dynabin.txt

mkdir myproject
cd myproject
python3 -m venv venv

Dependencies

These distributions will be installed automatically when installing Flask.

  • Werkzeug implements WSGI, the standard Python interface between applications and servers.
  • Jinja is a template language that renders the pages your application serves.
  • MarkupSafe comes with Jinja. It escapes untrusted input when rendering templates to avoid injection attacks.
  • ItsDangerous securely signs data to ensure its integrity. This is used to protect Flask’s session cookie.
  • Click is a framework for writing command line applications. It provides the flask command and allows adding custom management commands.

Optional dependencies

These distributions will not be installed automatically. Flask will detect and use them if you install them.

  • Blinker provides support for signals.
  • SimpleJSON is a fast JSON implementation that is compatible with Python’s json module. It is preferred for JSON operations if it is installed.
  • python-dotenv enables support for dotenv when running flask commands.
  • Watchdog provides a faster, more efficient reloader for the development server.

Virtual environments

Use a virtual environment to manage the dependencies for your project, both in development and in production.

What problem does a virtual environment solve? The more Python projects you have, the more likely it is that you need to work with different versions of Python libraries, or even Python itself. Newer versions of libraries for one project can break compatibility in another project.

Virtual environments are independent groups of Python libraries, one for each project. Packages installed for one project will not affect other projects or the operating system’s packages.

Python 3 comes bundled with the venv module to create virtual environments. If you’re using a modern version of Python, you can continue on to the next section.

If you’re using Python 2, see Install virtualenv first.

Create an environment

Create a project folder and a venv folder within:

mkdir myproject
cd myproject
python3 -m venv venv

On Windows:

py -3 -m venv venv

If you needed to install virtualenv because you are on an older version of Python, use the following command instead:

virtualenv venv

On Windows:

\Python27\Scripts\virtualenv.exe venv

Activate the environment

Before you work on your project, activate the corresponding environment:

. venv/bin/activate

On Windows:

venv\Scripts\activate

Your shell prompt will change to show the name of the activated environment.