{"id":15010365,"url":"https://github.com/chrovis/gnife","last_synced_at":"2026-04-04T06:05:09.016Z","repository":{"id":227463893,"uuid":"771498100","full_name":"chrovis/gnife","owner":"chrovis","description":"Gnife is a CLI tool for manipulating genomic files and data.","archived":false,"fork":false,"pushed_at":"2025-04-14T04:09:27.000Z","size":46,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":13,"default_branch":"main","last_synced_at":"2025-04-14T05:24:03.924Z","etag":null,"topics":["bioinformatics","clojure","genomics"],"latest_commit_sha":null,"homepage":"","language":"Clojure","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/chrovis.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","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":"2024-03-13T12:09:15.000Z","updated_at":"2025-04-14T04:09:24.000Z","dependencies_parsed_at":"2024-04-27T06:22:49.749Z","dependency_job_id":"7467698d-a34e-4778-a5a5-1458f9f82024","html_url":"https://github.com/chrovis/gnife","commit_stats":null,"previous_names":["chrovis/gnife"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/chrovis/gnife","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrovis%2Fgnife","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrovis%2Fgnife/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrovis%2Fgnife/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrovis%2Fgnife/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/chrovis","download_url":"https://codeload.github.com/chrovis/gnife/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrovis%2Fgnife/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28076814,"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","status":"online","status_checked_at":"2025-12-27T02:00:05.897Z","response_time":58,"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":["bioinformatics","clojure","genomics"],"created_at":"2024-09-24T19:33:43.071Z","updated_at":"2025-12-27T09:26:51.255Z","avatar_url":"https://github.com/chrovis.png","language":"Clojure","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Gnife [naɪf]\n[![build](https://github.com/chrovis/gnife/actions/workflows/build.yml/badge.svg)](https://github.com/chrovis/gnife/actions/workflows/build.yml)\n\nGnife is a CLI tool for manipulating genomic files and data.\n\n## Installation\n\n### Manual Install\n\nGnife requires you have installed Java. A binary are available on the\n[releases](https://github.com/chrovis/gnife/releases) page.\n\n```sh\ncurl -sSL https://github.com/chrovis/gnife/releases/download/0.1.3/gnife -o gnife\nchmod +x gnife\nmv gnife [/your/PATH/dir/]\n```\n\n### Homebrew\n\nYou can use [Homebrew](https://brew.sh/) on MacOS.\n\n```sh\nbrew install xcoo/formulae/gnife\n```\n\n### Build\n\nTo build Gnife manually, you must setup Clojure (and Java) in advance.\n\n```sh\nclojure -T:build bin\ncp target/gnife [/your/PATH/dir/]\n```\n\n## Getting Started\n\nEach Gnife command can be called by `gnife [type] [command]`.\n\n```console\n$ gnife hgvs repair \"c.123_124GC\u003eAA\"\nc.123_124delGCinsAA\n```\n\n## Command List\n\nGnife commands are grouped by data type. `gnife --tree` lists all commands in a\ntree-like format.\n\n```console\n$ gnife --tree\nsequence\n  dict   Create a sequence dictionary for a reference sequence\n  faidx  Index a reference sequence in the FASTA format\n\nsam\n  view       Extract/print all or sub alignments in SAM or BAM format\n  convert    Convert file format based on the file extension\n  normalize  Normalize references of alignments\n  sort       Sort alignments by leftmost coordinates\n  index      Index sorted alignment for fast random access\n  pileup     Generate pileup for the BAM file\n  level      Analyze a BAM file and add level information of alignments\n\nvcf\n  liftover  Convert genomic coordinates in a VCF file between assemblies\n\nvariant\n  liftover  Convert a genomic coordinate between assemblies\n  to-hgvs   Convert a VCF-style variant into HGVS\n\nhgvs\n  format      Format HGVS with a specified style\n  repair      Repair an invalid HGVS\n  to-variant  Convert a HGVS into VCF-style variants\n```\n\n`gnife [type] [command] --help` to display detailed usage of each command.\n\n## JVM Options\n\nTo pass extra arguments to the JVM, set the `GNIFE_JVM_OPTS` environment\nvariable.\n\n```sh\nexport GNIFE_JVM_OPTS=\"-XX:TieredStopAtLevel=1 -Xmx4g\"\n```\n\n## Test\n\nTo run tests,\n\n- `clojure -X:test` for basic tests, and\n- `clojure -X:test:slow-test` for slow tests with remote resources.\n\n## License\n\nCopyright 2024 [Xcoo, Inc.](https://xcoo.jp/)\n\nLicensed under the [Apache License, Version 2.0](LICENSE).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchrovis%2Fgnife","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchrovis%2Fgnife","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchrovis%2Fgnife/lists"}