{"id":18204683,"url":"https://github.com/jfallmann/trna_ngs_mod_map_call_galaxy","last_synced_at":"2026-01-19T06:33:51.009Z","repository":{"id":83607291,"uuid":"99226284","full_name":"jfallmann/tRNA_ngs_mod_map_call_galaxy","owner":"jfallmann","description":"Tool collection for identification of tRNA modifications from NGS data galaxy workflow","archived":false,"fork":false,"pushed_at":"2017-08-04T08:22:16.000Z","size":41,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-07T19:18:31.303Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/jfallmann.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":"2017-08-03T11:38:18.000Z","updated_at":"2024-06-09T18:47:45.000Z","dependencies_parsed_at":"2023-07-08T19:15:19.297Z","dependency_job_id":null,"html_url":"https://github.com/jfallmann/tRNA_ngs_mod_map_call_galaxy","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/jfallmann/tRNA_ngs_mod_map_call_galaxy","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jfallmann%2FtRNA_ngs_mod_map_call_galaxy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jfallmann%2FtRNA_ngs_mod_map_call_galaxy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jfallmann%2FtRNA_ngs_mod_map_call_galaxy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jfallmann%2FtRNA_ngs_mod_map_call_galaxy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jfallmann","download_url":"https://codeload.github.com/jfallmann/tRNA_ngs_mod_map_call_galaxy/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jfallmann%2FtRNA_ngs_mod_map_call_galaxy/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28562405,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-19T03:31:16.861Z","status":"ssl_error","status_checked_at":"2026-01-19T03:31:15.069Z","response_time":67,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: 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":[],"created_at":"2024-11-03T11:41:53.320Z","updated_at":"2026-01-19T06:33:50.994Z","avatar_url":"https://github.com/jfallmann.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# tRNA\\_ngs\\_mod\\_map\\_call\\_galaxy\n## Tool collection for identification of tRNA modifications from NGS data galaxy workflow\n\nThis git repo contains a collection of tools and\n[galaxy](https://galaxyproject.org/) wrappers for the\n[tRNA read mapping workflow](https://github.com/AnneHoffmann/tRNA-read-mapping)\nwhich can either be run from commandline or in galaxy.\n\n*Requires a local installation of gatk in version 3.6-0.*\n\nJust install gatk and link the GenomeAnalysisTK.jar to this directory.\n\nDue to this dependency and the corresponding issues with licensing,\nthis tool collection is not part of the galaxy toolshed.  This may\nchange in the future, due to the open source license for GATK4.\n\n\nMeanwhile, just clone this repository, link the GenomeAnalysisTK.jar\nexecutable into the tools directory and add the tools to your galaxy\ninstance.\n\nTo run this workflow you must also install the tRNA\\_prediction tool\nfrom the\n[galaxy toolshed](https://toolshed.g2.bx.psu.edu/view/bgruening/trna_prediction/358f58401cd6)\nand resolve all tool depencies.\n\n\nIn case you are using a docker image of galaxy, make sure that this\ndirectory is exported to galaxy and create a mytools.xml file, a file\n[mytools.xml.example](mytools.xml.example) is part of this repo.\n\n\n## A docker run example could look like this:\n\n\n```docker run -d -p 8080:80 -p 8021:21 -p 8800:8800 --privileged=true -v ${PATHtoStorage}/galaxy_storage/:/export/ -v ${PATHtoGits}/tRNA_ngs_mod_map_call_galaxy/:/tRNA_mods -e GALAXY_CONFIG_TOOL_CONFIG_FILE=config/tool_conf.xml,config/shed_tool_conf.xml,/tRNA_mods/mytools.xml ${dockerimageID}```\n\nMore information on how to include custom tools in galaxy can be found\nat the official galaxy documents,\ne.g. [here](https://galaxyproject.org/admin/tools/add-tool-tutorial/).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjfallmann%2Ftrna_ngs_mod_map_call_galaxy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjfallmann%2Ftrna_ngs_mod_map_call_galaxy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjfallmann%2Ftrna_ngs_mod_map_call_galaxy/lists"}