System Requirements

If you just want to generate layouts for the "standard mode" of MetagenomeScope (i.e. without using the -spqr option), you'll just need the General Requirements listed below.

However, if you want to generate layouts for the SPQR "decomposition mode" of MetagenomeScope (i.e. using the -spqr command-line option), there are some extra system requirements you'll have to follow in order for the preprocessing script to work properly. In this case, you'll need both the General Requirements and -spqr Requirements listed below.

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.
  • Other versions of Python 2.x should be ok, but Python 2.7 is recommended.
• 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.

-spqr Requirements

• The sfdp layout program contained in Graphviz
  • sfdp should usually be installed by default with Graphviz, fortunately.
• The GTS library (libgts-dev on Debian/Ubuntu systems)
  • The triangulation functionality provided by GTS is used by sfdp when generating layouts in the SPQR mode, in order to smooth things out.
  • If you don't want to install GTS, you can use the -nt argument to disable triangle smoothing in the SPQR mode. (This might make certain layouts in the SPQR mode appear more cluttered, though.)
• OGDF
  • OGDF is linked with the "SPQR script" (graph_collator/spqr.cpp) that is used by the preprocessing script to generate SPQR tree information.
  • If you're using a non-64-bit Linux system, you're going to need to compile your own binary of the SPQR script using the Makefile included in the root of MetagenomeScope. See the installation page of this wiki for information on downloading and building OGDF to do that.