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https://github.com/ciw-project-2023/coaler
CoAler = Core Aligner (Multi-Alignment of Molecules)
https://github.com/ciw-project-2023/coaler
alignment bioinformatics conan cpp rdkit
Last synced: 3 months ago
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CoAler = Core Aligner (Multi-Alignment of Molecules)
- Host: GitHub
- URL: https://github.com/ciw-project-2023/coaler
- Owner: ciw-project-2023
- Created: 2023-10-27T08:39:52.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2024-05-15T10:27:34.000Z (8 months ago)
- Last Synced: 2024-10-31T12:39:53.268Z (3 months ago)
- Topics: alignment, bioinformatics, conan, cpp, rdkit
- Language: C++
- Homepage:
- Size: 23.2 MB
- Stars: 8
- Watchers: 0
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# coaler
**For examples see the [paper](https://github.com/ciw-project-2023/coaler/blob/main/paper.pdf)**
Core Aligner
## Building locally
To build the project locally, you need to have a valid GCC installation as well as
python (>3.10 with venv support) installed. You can build the project with the following commands:
```bash
./confgiure
make
sudo make install
````
The configure script will create a virtual environment in the `venv` directory and install the conan package manager.
The make targets will use conan to build the project. The binary will be installed to `/usr/local/bin/coaler`. You might
have to add `/usr/local/bin` to your `PATH` variable.
### Building Containerized
If you want to use Podman to run the application, you can use the following command:
```bash
make container
```
This will build an container image with the name `coaler:latest`. You can run the container with the following command:
```bash
./run.sh
```
The script will mount the current directory to your PWD in the container and run the application passing all arguments to it.
### Setup Clion
In the output of `conan build` you should get an output containing lines like this:
```
======== Calling build() ========
conanfile.py (aligner/0.0.1): Calling build()
conanfile.py (aligner/0.0.1): Running CMake.configure()
conanfile.py (aligner/0.0.1): RUN: cmake -G "Unix Makefiles" -DCMAKE_TOOLCHAIN_FILE="/home/niklas/projects/uni/coaler/build/Debug/generators/conan_toolchain.cmake" -DCMAKE_INSTALL_PREFIX="/home/niklas/projects/uni/coaler" -DCMAKE_POLICY_DEFAULT_CMP0091="NEW" -DCMAKE_BUILD_TYPE="Debug" "/home/niklas/projects/uni/coaler"
```
Copy this part (it will be different for on your PC):
```
-DCMAKE_TOOLCHAIN_FILE="/home/niklas/projects/uni/coaler/build/Debug/generators/conan_toolchain.cmake" -DCMAKE_INSTALL_PREFIX="/home/niklas/projects/uni/coaler" `
```
1. Open your Project in Clion and tell it that it is a CMake project
2. In Clion Goto Settings->Build,Execution...->CMAKE and add the thing you just copied to `CMake Options`.
3. Change "Build directory" from `cmake-build-debug` to `build` (Conan uses this one)
4. You'll get a CMake plugin tab in your plugins -> Run "Reload CMake"
5. If your build worked, this should work without error.
Now you should be able to see the RDKit headers you linked under `External Libraries -> Header Search Paths -> include`