{"id":20934688,"url":"https://github.com/biocore/q2-ili","last_synced_at":"2026-04-21T22:06:26.913Z","repository":{"id":137558042,"uuid":"153533918","full_name":"biocore/q2-ili","owner":"biocore","description":"QIIME2 plugin for `ili","archived":false,"fork":false,"pushed_at":"2018-10-18T22:17:19.000Z","size":4414,"stargazers_count":1,"open_issues_count":4,"forks_count":2,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-01-31T04:09:07.395Z","etag":null,"topics":["microbiome","qiime","visualization"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/biocore.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2018-10-17T22:57:01.000Z","updated_at":"2021-12-06T10:44:01.000Z","dependencies_parsed_at":null,"dependency_job_id":"5f84efec-47ca-47d4-a23a-957aab5f416f","html_url":"https://github.com/biocore/q2-ili","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biocore%2Fq2-ili","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biocore%2Fq2-ili/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biocore%2Fq2-ili/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biocore%2Fq2-ili/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biocore","download_url":"https://codeload.github.com/biocore/q2-ili/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243330262,"owners_count":20274037,"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":["microbiome","qiime","visualization"],"created_at":"2024-11-18T22:10:35.009Z","updated_at":"2025-12-28T22:49:45.782Z","avatar_url":"https://github.com/biocore.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# QIIME 2 \\`ili plugin\n\n[![Build Status](https://travis-ci.org/biocore/q2-ili.svg?branch=master)](https://travis-ci.org/biocore/q2-ili) [![Coverage Status](https://coveralls.io/repos/github/biocore/q2-ili/badge.svg?branch=master)](https://coveralls.io/github/biocore/q2-ili?branch=master)\n\nThis is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org.\n\nThis plugin is wrapping \\`ili, for more information, see https://github.com/MolecularCartography/ili.\n\n# Installation\n\nTo install `q2-ili` you need a working QIIME 2 installation. After you have\ninstalled QIIME 2, clone and install `q2-ili` by running these commands:\n\n```bash\ngit clone --recurse-submodules https://github.com/biocore/q2-ili.git \u0026\u0026 cd q2-ili\npip install .\nqiime dev refresh-cache\n```\n\n## Troubleshooting installation\n\nIf the `git` command above results in an error like the following:\n\n```bash\nerror: Server does not allow request for unadvertised object...\n```\n\nyou may need to update the version of `git` that is installed on your system. You can download the latest version of git [here](https://git-scm.com/downloads). \n\n# Requirements\n\nIn order to use this plugin, you need a 3D model in STL format and a mapping\nbetween your samples and their coordinate locations in the model. To do this\nyour QIIME 2 metadata file needs to include three columns labeled `x`, `y` and\n`z`. For more information see [\\`ili's\ndocumentation](https://github.com/MolecularCartography/ili).\n\n# Example\n\nTo exemplify how to use `q2-ili`, we will use the data from [Bouslimani et al.\n2015](http://www.pnas.org/content/112/17/E2120). The metabolomic features will\nbe colored in the model according to the site where they were collected from.\nThe data for this example is included in the `example-data` directory of the\nrepository you cloned above.\n\nFirst we need to import the model as a QIIME2 artifact. The type `Model` is\ninstalled in QIIME 2 along with this plugin, hence we can run the following\ncommand:\n\n```bash\nqiime tools import \\\n--type Model \\\n--input-path example-data/model.stl \\\n--output-path model.qza\n```\n\nNext, we generate the visualization using the model and the numeric data that\nwe have in the metadata file:\n\n```bash\nqiime ili plot \\\n--i-model model.qza \\\n--m-metadata-file example-data/metadata.tsv \\\n--o-visualization visualization.qzv\n```\n\nLastly, you can visualize and interact with this model using\n[q2view](https://view.qiime2.org).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiocore%2Fq2-ili","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiocore%2Fq2-ili","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiocore%2Fq2-ili/lists"}