System Requirements

As of January 11, 2018, there are two versions of the script: one which generates SPQR trees for biconnected components of assembly graphs to be used in the "SPQR Decomposition Mode" of MetagenomeScope, and one which does not. Both versions produce output that works with MetagenomeScope's "standard mode," but the SPQR version of the script has a few more requirements due to its use of a C++ script for generating SPQR trees.

General Requirements

• Python 2.7

  • Installed by default with many systems. Installation instructions for Python (as well as instructions for checking to see if you already have Python installed) are located here.

• NumPy

  • Installation instructions are located here.

• Graphviz, with the dot layout program installed

  • Using a version after 2.41.20170712.0019 is recommended (see this issue for details).
  • Download links and installation instructions are located here.

• PyGraphviz

  • Installation instructions are located here.
  • Depending on your system, it may be easiest to install PyGraphviz through pip or another Python package manager.
  • From personal experience, I found that installing pkg-config before installing PyGraphviz helped resolve issues I had with importing it. If you're having trouble getting PyGraphviz installed, looking over the comments in this issue in the PyGraphviz repository might be helpful.

Requirements specific to the SPQR version (graph_collator/collate.py)

• The sfdp layout program contained in Graphviz
  • sfdp should usually be installed by default with Graphviz, fortunately.
• OGDF
  • If you're using a non-64-bit Linux system, you're going to need to compile your own binary of the SPQR script. See the installation page of this wiki for information on downloading and building OGDF to do that.