Building
Note: All required executables are included with the release tarball,
available on the release page.
Download using the shapemapper-2.1.5.tar.gz
link, not the link for source code only.
Rebuilding should only be needed in very specialized cases.
Runtime dependencies
All third-party executables are included in the main release, within
the subdirectory internals/thirdparty
. If attempting to run from a
source-only release, these will need to be installed at the system level.
- bash
- python >= 3.5.3 (
python3
must be visible in the PATH) - threaded perl >= 5.22.0 (for bowtie2 wrapper)
- bowtie2 >= 2.3.0
- bbmap >= 37.78 (includes bbmerge), requires building JNI components
- jdk >= 8.0.45 (required for compiling bbmerge JNI components)
- java >= 8.0.45 (for bbmerge)
- matplotlib >= 1.5.1 (very recent versions might break some things)
- pipeviewer >= 1.6.0
- STAR aligner >= 2.5.2a (Optional. Only useful to speed up alignment against large target sequences.)
- scikit-learn >= 0.18.1 (Optional. Only needed if running ROC_tests.sh)
- graphviz >= 2.38.0 (Optional. only needed if running shapemapper with
--render-flowchart
option) - ghostscript >= 9.25 (Optional. For debugging use with --render-mutations)
Build requirements
- cmake >= 3.4.3
- gcc/g++ >= 5.3.0 (must support C++11)
- zlib
- boost >= 1.60.0 libs: filesystem, program_options, iostreams, system
- doxygen >= 1.8.10 (Optional. For rendering c++ documentation)
Building ShapeMapper binaries
To rebuild ShapeMapper executables
- Delete the folder
build
if present - Run
internals/bin/build_binaries.sh
or run the following commands, starting from inside the top-level shapemapper-2.1.5 folder:mkdir build
cd build
cmake ..
make
Source code documentation
- C++ documentation at
internals/cpp-src/doc/html/index.html
- Python documentation in source code comments (folder
internals/python
)