Python_GDC_DL

Created for CSI4900 - Honours Project

Python script that will request RNA-seq and miRNA-seq files from the GDC server

GDC search and retieval API documentation: https://docs.gdc.cancer.gov/API/Users_Guide/Search_and_Retrieval/

My related scripts:

https://github.com/bbpgrs/Python_GDC_Integration

https://github.com/bbpgrs/Python_GDC_Plot

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Python 3 is required, Python 3.6 or higher strongly recommended (not tested with older versions).

https://www.python.org/downloads/release

Running this program through the command line is recommended as IDEs may need extra configuration.

Run program:

Windows (Python 3 installed)

python main.py

Linux/MacOS

python3 main.py

Commandline arguments:

Only generate file manifest lists (download files later)

python main.py -man

Only download files (use previously generated manifest lists)

python main.py -dlo

If both arguments are provided '-man' will be used.

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This program requires the 'requests' library: http://docs.python-requests.org/en/latest/user/install/

To install the 'requests' library:

Windows:

Check for pip updates

python -m pip install --upgrade pip

Install pipenv

python -m pip install pipenv

Install requests

python -m pipenv install requests

Mac OS:

Same commands as above, but use 'python3' instead,

OR (not tested):

Install Python 3: http://docs.python-guide.org/en/latest/starting/install3/osx/ 

Installing Python 3 using Homebrew as described in the guide will also install pip3.

Then:

> pip3 install pipenv

> pipenv install requests

Linux:

Same commands as above (Windows), but use 'python3' instead,

OR (not tested):

Install pip for Python 3 (Debian Linux)

> sudo apt-get install python3-pip

Then:

> pip3 install pipenv

> pipenv install requests

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Copyright (C) 2018 Ahmad A. A.