{"id":37723807,"url":"https://github.com/zavolanlab/zarp-cli","last_synced_at":"2026-01-16T13:36:18.187Z","repository":{"id":40486578,"uuid":"342518944","full_name":"zavolanlab/zarp-cli","owner":"zavolanlab","description":"A user-friendly command-line interface for the ZARP RNA-seq analysis workflow","archived":false,"fork":false,"pushed_at":"2025-08-26T11:13:20.000Z","size":44969,"stargazers_count":5,"open_issues_count":10,"forks_count":1,"subscribers_count":4,"default_branch":"dev","last_synced_at":"2025-10-29T10:42:43.589Z","etag":null,"topics":["bioinformatics","cli","command-line-interface","fair","high-throughput","library","pipeline","python","reproducible-research","rna-seq","sequencing","snakemake","transcriptomics","workflow"],"latest_commit_sha":null,"homepage":"https://zavolanlab.github.io/zarp-cli/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/zavolanlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2021-02-26T09:01:18.000Z","updated_at":"2024-11-01T11:27:51.000Z","dependencies_parsed_at":"2024-02-11T13:22:52.695Z","dependency_job_id":"802a60db-fc4b-4b27-95ec-d4036ec95023","html_url":"https://github.com/zavolanlab/zarp-cli","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/zavolanlab/zarp-cli","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zavolanlab%2Fzarp-cli","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zavolanlab%2Fzarp-cli/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zavolanlab%2Fzarp-cli/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zavolanlab%2Fzarp-cli/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/zavolanlab","download_url":"https://codeload.github.com/zavolanlab/zarp-cli/tar.gz/refs/heads/dev","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zavolanlab%2Fzarp-cli/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28479033,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T11:59:17.896Z","status":"ssl_error","status_checked_at":"2026-01-16T11:55:55.838Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["bioinformatics","cli","command-line-interface","fair","high-throughput","library","pipeline","python","reproducible-research","rna-seq","sequencing","snakemake","transcriptomics","workflow"],"created_at":"2026-01-16T13:36:18.090Z","updated_at":"2026-01-16T13:36:18.174Z","avatar_url":"https://github.com/zavolanlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ZARP-cli\n\n[![License][badge-license]][badge-url-license]\n[![Build_status][badge-build-status]][badge-url-build-status]\n[![Docs][badge-docs]][badge-url-docs]\n[![Coverage][badge-coverage]][badge-url-coverage]\n[![GitHub_tag][badge-github-tag]][badge-url-github-tag]  \n[![DOI:zenodo][badge-doi-zenodo]][badge-url-doi-zenodo]\n[![DOI:f1000][badge-doi-f1000]][badge-url-doi-f1000]\n\n:pill: **_ZARP_** - RNA-Seq analysis made easy! :syringe:\n\n## Synopsis\n\n- You have a bunch of RNA-Seq samples and wanna know what's in them? **_ZARP\n'em!_**  \n- You have an extensive SRA query with hundreds of runs and you don't know\nwhere to start? **Easy - _ZARP 'em!_**\n- Barry left you some samples to analyze and then went on vacation, again? **No\nproblem, _ZARP 'em!_**  \n\nZARP-cli uses the [HTSinfer][htsinfer] package to infer missing metadata and\nthen runs the [ZARP RNA-Seq analysis pipeline][zarp] on your samples. Impress\nyour colleagues with your sudden productivity boost. Or better yet, use the\ntime saved to go on that camping trip with Barry. Just make sure to guard your\nsecret! :wink:\n\n## Basic usage\n\n```sh\nzarp [-h] [--init] [--verbosity {DEBUG,INFO,WARN,ERROR,CRITICAL}] [--version]\n        PATH/ID [PATH/ID ...]\n\n# Examples\nzarp --init  # set up user defaults for ZARP\nzarp sample_1.fq.gz /path/to/sample_2.fq.gz  # ZARP two single-end libraries\nzarp my_sample@abcdefgh.fq.gz  # assign a sample name\nzarp mate_1.fq.gz,mate_2.fq.gz  # ZARP one paired-end library\nzarp table:table.tsv  # ZARP all samples from a sample table\nzarp SRR0123456789 my_other_sample@SRR0123456789  # ZARP SRA runs\nzarp \\\n    sample_1.fq.gz /path/to/sample_2.fq.gz \\\n    my_sample@adcdefgh.fg.gz \\\n    mate_1.fq.gz,mate_2.fq.gz \\\n    table:table.tsv \\\n    SRR0123456789 my_other_sample@SRR0123456789  # ZARP everything at once!\n```\n\n## Quick installation\n\nQuick installation requires the following:\n\n- Linux with root permissions\n- [`conda \u003e= 22.11.1`][conda]\n- [`mamba \u003e=1.3.0`][mamba]\n\nExecute the following commands:\n\n```sh\ngit clone git@github.com:zavolanlab/zarp\ngit clone git@github.com:zavolanlab/zarp-cli.git\ncd zarp-cli\nmamba env create -f install/environment.root.yml\nconda activate zarp-cli\n```\n\n\u003e If you do not have root privileges on your machine, replace the `mamba env\n\u003e create` call with the following one:\n\u003e\n\u003e ```sh\n\u003e mamba env create -f install/environment.yml\n\u003e ```\n\nThat's it - you can now use _ZARP-cli_!\n\n## Documentation\n\nWe have designed _ZARP-cli_ to be easy to use. However, there are still a lot\nof ways in which execution can be tweaked. For the full documentation visit\n**\u003chttps://zavolanlab.github.io/zarp-cli\u003e**.\n\n## Versioning\n\nThe project adopts the [Semantic Versioning][semver] specification for\nversioning. Currently the service is still in beta stage, so the API may change\nand even break without further notice. However, we are planning to release a\n`1.0.0` release as soon as we feel that the software is reasonably stable and\n\"feature complete\" for all of the major use cases we wish to cover.\n\n## Contributing\n\nThis project lives off your contributions, be it in the form of bug reports,\nfeature requests, discussions, or fixes and other code changes. Please refer\nto the [contributing guidelines](CONTRIBUTING.md) if you are interested to\ncontribute. Please mind the [code of conduct](CODE_OF_CONDUCT.md) for all\ninteractions with the community.\n\n## Contact\n\nFor questions or suggestions regarding the code, please use the\n[issue tracker][issue-tracker]. For any other inquiries, please contact us\nby [email][contact].\n\n\u0026copy; 2021 [Zavolab, Biozentrum, University of Basel][zavolab]\n\n[conda]: \u003chttps://docs.conda.io/projects/conda/en/latest/index.html\u003e\n[contact]: \u003cmailto:zavolab-biozentrum@unibas.ch\u003e\n[badge-build-status]: \u003chttps://github.com/zavolanlab/zarp-cli/actions/workflows/tests.yml/badge.svg\u003e\n[badge-coverage]: \u003chttps://codecov.io/gh/zavolanlab/zarp-cli/branch/dev/graph/badge.svg?branch=dev\u0026token=0KQZYULZ88\u003e\n[badge-docs]: \u003chttps://github.com/zavolanlab/zarp-cli/actions/workflows/docs.yml/badge.svg\u003e\n[badge-doi-zenodo]: \u003chttps://img.shields.io/badge/Zenodo-10.5281%2Fzenodo.10789818-informational\u003e\n[badge-doi-f1000]: \u003chttps://img.shields.io/badge/F1000Research-10.12688%2Ff1000research.149237.1-informational\u003e\n[badge-github-tag]: \u003chttps://img.shields.io/github/v/tag/zavolanlab/zarp-cli?color=C39BD3\u003e\n[badge-license]: \u003chttps://img.shields.io/badge/license-Apache%202.0-blue.svg\u003e\n[badge-url-build-status]: \u003chttps://github.com/zavolanlab/zarp-cli/actions/workflows/tests.yml\u003e\n[badge-url-coverage]: \u003chttps://codecov.io/gh/zavolanlab/zarp-cli?branch=dev\u003e\n[badge-url-docs]: \u003chttps://zavolanlab.github.io/zarp-cli\u003e\n[badge-url-doi-zenodo]: \u003chttps://doi.org/10.5281/zenodo.10789818\u003e\n[badge-url-doi-f1000]: \u003chttps://doi.org/10.12688/f1000research.149237.1\u003e\n[badge-url-github-tag]: \u003chttps://github.com/zavolanlab/zarp-cli/releases\u003e\n[badge-url-license]: \u003chttp://www.apache.org/licenses/LICENSE-2.0\u003e\n[htsinfer]: \u003chttps://github.com/zavolanlab/htsinfer\u003e\n[issue-tracker]: \u003chttps://github.com/zavolanlab/zarp-cli/issues\u003e\n[mamba]: \u003chttps://mamba.readthedocs.io/en/latest/\u003e\n[semver]: \u003chttps://semver.org/\u003e\n[zarp]: \u003chttps://github.com/zavolanlab/zarp\u003e\n[zavolab]: \u003chttps://www.biozentrum.unibas.ch/research/researchgroups/overview/unit/zavolan/research-group-mihaela-zavolan/\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzavolanlab%2Fzarp-cli","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fzavolanlab%2Fzarp-cli","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzavolanlab%2Fzarp-cli/lists"}