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

8

9)

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Download

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 Configure

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Examples

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License

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Panel
titleDownload and Configuration

Public Use (v0.1.

7

8 released

June 9

Sept 27 2016)

  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

 

No Format
{
  "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"
    }
  ]
}

Internal to Broad Institute

  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