Prerequisite packages
To download, build and run the shasta software on a
Ubuntu (16.04, 18.04, 20.04) or macOS (10.14, 10.15) machine, the following packages are required:
| Package | Ubuntu package name | Needed to build from source? | Needed to run assembly? | Used by http server? | Comments |
|---|---|---|---|---|---|
| Git | git | Only needed to get the source code from GitHub. | |||
| The g++ compiler | g++ | ✔ | ✔ | ✔ | Runtime libraries only needed at run time. |
| Cmake | cmake | ✔ | |||
| The Boost libraries | libboost-dev | ✔ | |||
| Graphviz | graphviz | ✔ | Used for graph layout. | ||
| Blast | ncbi-blast+ | ✔ | Used by the http server for interactively computing alignments. | ||
| Python 3 | python3 | ✔ | ✔ | ✔ | |
| pip3 | pip3 | Only needed to install pybind11 (see below)
| |||
| Pybind11 | pybind11 (pip3 package) | ✔ | Used to provide Python bindings to C++ code. | ||
| The png library | libpng-dev | ✔ | ✔ | ✔ | Used to display marker alignments in the http server. But it is a dependency of shasta.so, so it must be installed whether it is used or not.
|
| SeqAn 2.4.0 | ✔ | See InstallPrerequisites-Ubuntu.sh & InstallPrerequisites-macOS.sh for installation from GitHub.
| |||
| SPOA 3.4.0 | ✔ | See InstallPrerequisites-Ubuntu.sh & InstallPrerequisites-macOS.sh for installation from GitHub.
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