{"id":50699533,"url":"https://github.com/cbig/zig3-compilation-scripts","last_synced_at":"2026-06-09T08:32:27.953Z","repository":{"id":12850141,"uuid":"15526007","full_name":"cbig/zig3-compilation-scripts","owner":"cbig","description":"Instructions and scripts for dynamic compilation of Zonation on Linux","archived":false,"fork":false,"pushed_at":"2014-04-14T06:13:03.000Z","size":132,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":5,"default_branch":"master","last_synced_at":"2024-03-27T02:06:24.483Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","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/cbig.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}},"created_at":"2013-12-30T10:53:58.000Z","updated_at":"2024-03-27T02:06:24.484Z","dependencies_parsed_at":"2022-08-28T05:31:17.747Z","dependency_job_id":null,"html_url":"https://github.com/cbig/zig3-compilation-scripts","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/cbig/zig3-compilation-scripts","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbig%2Fzig3-compilation-scripts","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbig%2Fzig3-compilation-scripts/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbig%2Fzig3-compilation-scripts/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbig%2Fzig3-compilation-scripts/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cbig","download_url":"https://codeload.github.com/cbig/zig3-compilation-scripts/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbig%2Fzig3-compilation-scripts/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34098931,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-09T02:00:06.510Z","response_time":63,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2026-06-09T08:32:26.178Z","updated_at":"2026-06-09T08:32:27.946Z","avatar_url":"https://github.com/cbig.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Dynamic compilation of Zonation\n\nThese instruction describe the dynamic compilation of Zonation 3.1.11 on Ubuntu 13.04 (Raring Ringtail). Instructions have not been tested on other distributions/versions. You can copy the commands from this file or run the individual steps with the accompanied bash scripts. \n\nYou execute all steps by running:\n\n```\n./00-run-all\n```\n\n### 1. Install Zonation dependencies\n\n```\nsudo apt-get update\nsudo apt-get install cmake libqt4-dev libfftw3-dev libqwt-dev libboost-all-dev libgdal-dev\n``` \n\nAlternatively, run:\n\n```\n./01-deps-zig3\n```\n\n### 2. Get Zonation sources\n\nCreate a suitable download directory, fetch Zonation source code (version 3.1.11) from CBIG server, and extract the sources to the directory created:\n\n```\nmkdir zonation3\ncd zonation3\nwget http://cbig.it.helsinki.fi/files/zonation/zig3-src/zig3-3.1.11-src.tar.bz2\ntar -jxvf zig3-3.1.11-src.tar.bz2\n```\n\nAlternatively, run:\n\n```\n./02-wget-zig3\n```\n\n### 3. Build Zonation\n\nTo build Zonation library (`zig3lib`) and Zonation CLI utility (`zig3`), do the following:\n\n```\nmkdir zonation3/build\ncd zonation3/build\ncmake ../src-3\nmake\n```\n\nIf you have several cores available for compilation, you can pass switch `-j X` to `make` where `X` is the number of designated cores (e.g. `make -j 4`).\n\nAlternatively, run:\n\n```\n./03-build-zig3\n```\n\n### 4. Make Zonation available system wide (optional)\n\nIn order to call `zig3` anywhere on the system (instead of just the build-location), create a symbolic link:\n\n```\nsudo ln -s FULL_PATH/zonation3/build/zig3/zig3 /usr/local/bin/zig3\n```\n\nReplace `FULL_PATH` with the full path to the directory containing directory `zonation3` created in step 2.\n\nAlternatively, run:\n\n```\n./04-postinstall-zig3\n```\n\n## Testing Zonation using the tutorial data\n\nThis stage is completely optional.\n\nYou can test that Zonation works by running some of the runs used in the [Hunter Valley tutorial](https://github.com/cbig/zonation-tutorial). This is not a thorough test, but it will at least give you an overview on whether Zonationis working as intended. Tutorial data and setup files are fetched using [git](http://git-scm.com/) and run using [zrunner](https://github.com/cbig/zrunner).\n\n### 5. Install zrunner dependencies\n\nFirst, install git:\n\n```\nsudo apt-get -y install git\n```\n\nThen, install Python packages needed by zrunner:\n\n```\nsudo apt-get -y install python-yaml python-pip \n```\n\nAlternatively, run:\n\n```\n./05-deps-zrunner\n```\n\n### 6. Install zrunner\n\nzrunner is installed directly from GitHub using [pip](http://www.pip-installer.org/en/latest/).\n\n```\nsudo pip install https://github.com/cbig/zrunner/archive/master.zip\n```\n\nAlternatively, run:\n\n```\n./06-install-zrunner\n```\n\n### 7. Clone Zonation tutorial using git\n\nWith git installed, clone the tutorial repository with the following command:\n\n```\ngit clone https://github.com/cbig/zonation-tutorial.git\n``` \n\nAlternatively, run:\n\n```\n./07-git-tutorial\n```\n\n### 8. Run the tutorial runs\n\nYou can run [5 basic tutorial variants](https://github.com/cbig/zonation-tutorial/tree/master/basic) defined in the configuration file [`tutorial_runs.yaml`](https://github.com/cbig/zig3-compilation-scripts/blob/master/tutorial_runs.yaml) in this repository (note that similar file is found from within the tutorial repository as well) by using zrunner:\n\n```\nzrunner -l tutorial_runs.yaml\n```\n\nzrunner will produce an output file `results_XXX.yaml` in the same folder. `XXX` will correspond to information about your system. If everything went fine, you should see no critical errors on the screen and the yaml-file should report execution times for successful runs.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbig%2Fzig3-compilation-scripts","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcbig%2Fzig3-compilation-scripts","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbig%2Fzig3-compilation-scripts/lists"}