{"id":15017894,"url":"https://github.com/ciw-project-2023/coaler","last_synced_at":"2025-04-12T12:52:44.422Z","repository":{"id":204241880,"uuid":"710695295","full_name":"ciw-project-2023/coaler","owner":"ciw-project-2023","description":"CoAler = Core Aligner (Multi-Alignment of Molecules)","archived":false,"fork":false,"pushed_at":"2024-05-15T10:27:34.000Z","size":24313,"stargazers_count":8,"open_issues_count":0,"forks_count":1,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-03-26T07:36:34.743Z","etag":null,"topics":["alignment","bioinformatics","conan","cpp","rdkit"],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ciw-project-2023.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-10-27T08:39:52.000Z","updated_at":"2024-05-16T11:16:37.000Z","dependencies_parsed_at":null,"dependency_job_id":"43df4808-1eaf-4bf7-ad8a-8a179d9dc275","html_url":"https://github.com/ciw-project-2023/coaler","commit_stats":{"total_commits":337,"total_committers":12,"mean_commits":"28.083333333333332","dds":0.6706231454005935,"last_synced_commit":"b0ef31c2ffa37bcc2e033f944e3d326e87fecaec"},"previous_names":["ciw-project-2023/rdkitskeletoncpp","ciw-project-2023/coaler"],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ciw-project-2023%2Fcoaler","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ciw-project-2023%2Fcoaler/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ciw-project-2023%2Fcoaler/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ciw-project-2023%2Fcoaler/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ciw-project-2023","download_url":"https://codeload.github.com/ciw-project-2023/coaler/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248571636,"owners_count":21126520,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["alignment","bioinformatics","conan","cpp","rdkit"],"created_at":"2024-09-24T19:51:08.922Z","updated_at":"2025-04-12T12:52:44.401Z","avatar_url":"https://github.com/ciw-project-2023.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# coaler\n\n\u003cimg src=\"logo/coaler-removebg.png\" width=\"150\"\u003e\n\n**For examples see the [paper](https://github.com/ciw-project-2023/coaler/blob/main/paper.pdf)**\n\n\nCore Aligner\n\n## Building locally\n\nTo build the project locally, you need to have a valid GCC installation as well as\npython (\u003e3.10 with venv support) installed. You can build the project with the following commands:\n\n```bash\n./confgiure\nmake\nsudo make install\n````\n\nThe configure script will create a virtual environment in the `venv` directory and install the conan package manager.\nThe make targets will use conan to build the project. The binary will be installed to `/usr/local/bin/coaler`. You might\nhave to add `/usr/local/bin` to your `PATH` variable.\n\n### Building Containerized\nIf you want to use Podman to run the application, you can use the following command:\n\n```bash\nmake container\n```\n\nThis will build an container image with the name `coaler:latest`. You can run the container with the following command:\n\n```bash\n./run.sh\n```\n\nThe script will mount the current directory to your PWD in the container and run the application passing all arguments to it.\n\n### Setup Clion\n\nIn the output of `conan build` you should get an output containing lines like this:\n\n```\n======== Calling build() ========\nconanfile.py (aligner/0.0.1): Calling build()\nconanfile.py (aligner/0.0.1): Running CMake.configure()\nconanfile.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\"\n```\n\nCopy this part (it will be different for on your PC):\n\n```\n-DCMAKE_TOOLCHAIN_FILE=\"/home/niklas/projects/uni/coaler/build/Debug/generators/conan_toolchain.cmake\" -DCMAKE_INSTALL_PREFIX=\"/home/niklas/projects/uni/coaler\" `\n```\n\n1. Open your Project in Clion and tell it that it is a CMake project\n2. In Clion Goto Settings-\u003eBuild,Execution...-\u003eCMAKE and add the thing you just copied to `CMake Options`.\n3. Change \"Build directory\" from `cmake-build-debug` to `build` (Conan uses this one)\n4. You'll get a CMake plugin tab in your plugins -\u003e Run \"Reload CMake\"\n5. If your build worked, this should work without error.\n\nNow you should be able to see the RDKit headers you linked under `External Libraries -\u003e Header Search Paths -\u003e include`\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fciw-project-2023%2Fcoaler","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fciw-project-2023%2Fcoaler","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fciw-project-2023%2Fcoaler/lists"}