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2. Installing the software

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Nidhi Shah edited this page Mar 8, 2021 · 6 revisions

Installing MetaCarvel is very easy. To install and run MetaCarvel, you will need following dependancies:

You can install Networkx as described here. Briefly, you need to run the following:

pip install networkx>=2.5

If this doesn't work, you can download the source from here and install it from the source.

We use Open Graph Drawing Library (OGDF) in our code, but we are distributing that code with MetaCarvel since newer versions of OGDF library have different architecture and it can be hard to install MetaCarvel while setting all the paths correctly.

To install MetaCarvel, you simply need to run

git clone --recursive  https://github.com/marbl/MetaCarvel.git
cd MetaCarvel
bash install.sh

This would first install the OGDF library and then compile MetaCarvel code. And that's it! You are ready to run MetaCarvel!

NOTE: If you want to generate a visualization of the graphs generated by MetaCarvel, please follow the instructions to install MetagenomeScope here. MetagenomeScope will be downloaded as a submodule while downloading MetaCarvel, but you need to install it manually. Installing MetagenomeScope is not necessary if you just want to get scaffolds from MetaCarvel.

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