# KisSplice
Main page: http://kissplice.prabi.fr/
[User guide](https://gitlab.inria.fr/erable/kissplice/-/jobs/artifacts/master/file/prefix/share/doc/kissplice/user_guide.pdf?job=check_install_and_user_guide) from latest build.
# Docker
You can find the latest version of KisSplice, KisSplice2RefGenome and KissDE [on Docker Hub](https://hub.docker.com/repository/docker/dwishsan/kissplice-pipeline).
We also propose a [stand-alone Docker image for the KissDE Shiny App](https://hub.docker.com/repository/docker/dwishsan/kde-shiny) for KisSplice results exploration.
# Building:
Required:
- cmake >= 3.1
- C/C++11 compiler toolchain (binutils, gcc or clang)
- python3 to run kissplice
Recommended but optional:
- [bcalm](https://github.com/GATB/bcalm) >= v2.2.2 ; as a fallback a locally compiled version of bcalm can be used by passing `-DUSE_BUNDLED_BCALM=TRUE` to cmake. A debian/ubuntu package is available.
- latex toolchain with standard packages to build the user_guide ; this can be disabled by passing `-DUSER_GUIDE=OFF` to cmake
```
git clone https://gitlab.inria.fr/erable/kissplice
cd kissplice/
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make -j 4
```
After build the user guide (if not disabled) can be found in `build/doc/user_guide.pdf`.
The tool can be installed to a custom directory (like `~/.local/`) with:
```
cmake -DCMAKE_INSTALL_PREFIX=<directory> ..
make
make install
```
# Running on the sample test:
```
cd kissplice/build
./bin/kissplice -r ../sample_example/mock1.fq -r ../sample_example/mock2.fq -r ../sample_example/virus1.fq -r ../sample_example/virus2.fq
```