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updated name and instructions
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afrubin committed Mar 30, 2020
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# mavedb-convert
A command line tool for converting alternate file formats into a MaveDB compliant format.
# mavedbconvert
A command line tool for converting Multiplex Assay of Variant Effect datasets into a MaveDB-ready format.

# Installation
Download the `mavedb-convert` source and navigate to that directory.
Download the mavedbconvert source and navigate to that directory.
We recommend creating a [virtual environment](https://docs.python.org/3/library/venv.html) before proceeding with the installation.

Install dependencies using the requirements file and then install the package:
Install the package using pip:

pip3 install -r requirements/install.txt
pip3 install .

Additional requirements needed for running the unit tests and doing package development are in `reuirements/dev.txt`

## Troubleshooting
If you are a OSX user, you may experience header related issues when installing `pysam`. The current workaround
is to install pysam version `0.13` manually before installing the requirements:
If you are a OSX user, you may experience header related issues when installing pysam. The current workaround
is to install pysam v0.13 manually before installing the requirements:

pip install pysam==0.13
pip3 install pysam==0.13

This is the latest version known to compile without errors.

Although `pysam` is not required for `mavedb-convert` directly, it is installed by some of our dependencies. Until it is removed or made optional by those libraries, `mavedb-convert` will unfortunately not be installable on Windows.
Although pysam is not required for mavedbconvert directly, it is installed by some of our dependencies.
Until it is removed or made optional by those libraries, mavedbconvert will unfortunately not be installable on Windows.

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