diff --git a/README.md b/README.md index d12bdc4..fb1d7c3 100644 --- a/README.md +++ b/README.md @@ -1,23 +1,21 @@ -# 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.