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Python and UNIX CLI wrappers for FireBrowse API (version 0.1.

11)

Public Use (v0.1.

11 released Oct 31 2017)

1. Obtain Python 2.7 and the Requests package, both of which are likely to already be on your system. The internal versions used at the Broad Institute are Python 2.7.9 and Requests 2.5.1. Finally, we recommend installing to a Python virtual environment.
2. Download and install the PyPI package automatically with

linux% pip install firebrowse

  OR from this page with

This fbget zipfile, followed by these steps:

linux% unzip fbget-<version>.zip
linux% cd fbget-<version>
linux% sh install.sh
linux% python smoketest.py

  The smoketest is optional, but if the installation worked then it should return something like

{
  "HeartBeat": [
    "FireBrowse API at firebrowse.org:8000 is alive\n"
  ]
}
{
  "Reports": [
    {
      "cohort": "ACC",
      "data_type": [
        "CopyNumber"
      ],
      "date": "Fri, 17 Oct 2014 00:00:00 GMT",
      "file_type": "report",
      "report_name": "CopyNumber_Gistic2",
      "report_type": "CopyNumber",
      "report_uri": "http://gdac.broadinstitute.org/runs/analyses__2014_10_17/reports/cancer/ACC-TP/CopyNumber_Gistic2/nozzle.html",
      "sample_type": "TP"
    }
  ]
}
...

1. Ensure that /xchip/tcga/Tools/gdac/bin is in your $PATH. This is sufficient for using the fbget UNIX CLI tool. 
   
   
2. If you also want to use the Python bindings:
   
   
1. Ensure you are configured to use Python 2.7, then do either
   
   linux% eval setenv `gdac_pythonify` (t)csh
   or
   linux% export `gdac_pythonify` (ba)sh
   
   
2. Then run python
   
   linux% python
   
   
3. and import EITHER the low level wrappers
   
   python> import firebrowse
   
   
4. OR the high level wrappers
   
   python> import fbget