conda install -c bioconda panmap
This installs panmap and panmanUtils.
docker pull alanalohaucsc/panmap:latest
docker run --rm alanalohaucsc/panmap:latest --help
To run on local files, mount a volume:
docker run --rm -v $(pwd):/data -w /data alanalohaucsc/panmap:latest \
ref.panman reads.fq -o sample
| Package | Ubuntu/Debian |
|---|---|
| CMake >= 3.14 | cmake |
| C++17 compiler | g++ or clang++ |
| Protobuf | protobuf-compiler, libprotobuf-dev |
| Boost | libboost-program-options-dev, libboost-iostreams-dev, libboost-filesystem-dev, libboost-system-dev, libboost-date-time-dev |
| zlib | zlib1g-dev |
| htslib | libhts-dev |
| Cap’n Proto | capnproto, libcapnp-dev |
| Eigen3 | libeigen3-dev |
cmake -S . -B build -DCMAKE_BUILD_TYPE=Release
cmake --build build -j$(nproc)
The binary is at build/bin/panmap.