{"id":22731092,"url":"https://github.com/genentech/absolve","last_synced_at":"2025-04-14T00:32:42.984Z","repository":{"id":72633377,"uuid":"148548980","full_name":"Genentech/Absolve","owner":"Genentech","description":"Absolve antibody variable domain sequence analysis","archived":false,"fork":false,"pushed_at":"2018-09-13T22:39:17.000Z","size":6340,"stargazers_count":14,"open_issues_count":0,"forks_count":8,"subscribers_count":15,"default_branch":"master","last_synced_at":"2023-10-26T05:44:02.551Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Genentech.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"COPYING","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2018-09-12T22:18:02.000Z","updated_at":"2023-10-11T02:39:29.000Z","dependencies_parsed_at":"2023-04-27T03:56:47.568Z","dependency_job_id":null,"html_url":"https://github.com/Genentech/Absolve","commit_stats":null,"previous_names":[],"tags_count":0,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FAbsolve","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FAbsolve/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FAbsolve/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FAbsolve/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Genentech","download_url":"https://codeload.github.com/Genentech/Absolve/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":229117070,"owners_count":18022819,"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":[],"created_at":"2024-12-10T19:19:24.233Z","updated_at":"2024-12-10T19:19:25.119Z","avatar_url":"https://github.com/Genentech.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"_____________________________________________________________________________\n_____________________________________________________________________________\n\n# Absolve\n\nAbsolve is a command line tool for annotating antibody variable domain sequences with \n\n\t*  ORF\n\t*  Framework and CDR regions\n\t*  Kabat Numbering\n\t*  Germline Assignment\n\t*  Somatic Hypermutation \n\nAbsolve accepts fasta files as input, or fastq files as either single or paired-end reads.  It generates results for the input sequences as either a single tab-delimited file or multiple tab-delimited files if requested.  Germline sequences are provided for human, but users maybe provide their own fasta formatted database files that have been indexed by BWA.  \n\nAbsolve is written in C++ and links directly to BWA and HMMR libraries included.\n\n_____________________________________________________________________________\n_____________________________________________________________________________\n\n# Documentation\n\nPlease examine the manual for more detailed documentation of program parameters and design\n\n## ./docs/manual/Absolve.html \n\n_____________________________________________________________________________\n_____________________________________________________________________________\n\n# Build the application\n\nSupported platforms:\n\t* Linux\n\t* Mac OSX\n\n1. Platform/OS dependencies:\n\t* C++11 compatible compiler\n\t* C mathematical library. (libm) \n\t* Compression library. (libz)\n\t* POSIX multithreading library. (libpthread) \n\t* Specific Boost libraries: boost_system, boost_filesystem, boost_iostreams, boost_regex\n\t* CMake Ver 3.5 or greater\n\t\n2. Build the included dependencies.  Copies of BWA and HMMR are included.\n```\n\tcd dep/\n\ttar -zxvf bwa-0.7.12.tar.gz\n\ttar -zxvf hmmer-3.1b2.tar.gz\n\tcd bwa-0.7.12/ \n\tmake\n\tcd ..\n\tcd hmmer-3.1b2/\n\t./configure\n\tmake \n\tcd ../..\n\n```\n\n\n3. Configure environment \n```\n\t\tsource ./SETUP.bash `pwd`\n```\n\n4. Build release version \n```\n\t\tcmake CMakeLists.txt\n\t\tmake clean\n\t\tmake\n```\n\n5. Make sure all tests run ok \n```\n\t\tcd test\n\t\tcp -R testrun.ref.template testrun.ref\n\t\t./RunTest.bash\n\t\tcd ..\n```\n\n6.\tInvoke *\"absolve.bash\"* to run\n\n_____________________________________________________________________________\n_____________________________________________________________________________\neof\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fabsolve","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgenentech%2Fabsolve","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fabsolve/lists"}