{"id":15019255,"url":"https://github.com/kiwiroy/p5-alien-muscle","last_synced_at":"2026-03-15T19:38:43.424Z","repository":{"id":56841017,"uuid":"252680962","full_name":"kiwiroy/p5-alien-muscle","owner":"kiwiroy","description":"Alien module to provide muscle","archived":false,"fork":false,"pushed_at":"2020-05-03T22:20:20.000Z","size":24,"stargazers_count":0,"open_issues_count":1,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-12-26T08:34:10.981Z","etag":null,"topics":["alien","bioinformatics","perl","perl5"],"latest_commit_sha":null,"homepage":"https://metacpan.org/pod/Alien::MUSCLE","language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/kiwiroy.png","metadata":{"files":{"readme":"README.md","changelog":"Changes","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-04-03T08:56:16.000Z","updated_at":"2020-05-03T22:20:23.000Z","dependencies_parsed_at":"2022-08-29T12:50:35.886Z","dependency_job_id":null,"html_url":"https://github.com/kiwiroy/p5-alien-muscle","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/kiwiroy/p5-alien-muscle","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kiwiroy%2Fp5-alien-muscle","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kiwiroy%2Fp5-alien-muscle/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kiwiroy%2Fp5-alien-muscle/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kiwiroy%2Fp5-alien-muscle/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kiwiroy","download_url":"https://codeload.github.com/kiwiroy/p5-alien-muscle/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kiwiroy%2Fp5-alien-muscle/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30550462,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-15T15:03:43.933Z","status":"ssl_error","status_checked_at":"2026-03-15T15:03:37.630Z","response_time":61,"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":["alien","bioinformatics","perl","perl5"],"created_at":"2024-09-24T19:53:13.872Z","updated_at":"2026-03-15T19:38:43.400Z","avatar_url":"https://github.com/kiwiroy.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"# NAME\n\nAlien::MUSCLE - Discover or easy install of MUSCLE\n\n# SYNOPSIS\n\n    use Alien::MUSCLE;\n    @cmd = Alien::MUSCLE-\u003emuscle_binary;\n    push @cmd, (-in =\u003e 'sequences.fa', -out =\u003e 'results.afa', @opts);\n    system { $cmd[0] } @cmd;\n\nOr using [Bio::Tools::Run::Alignment::Muscle](https://metacpan.org/pod/Bio%3A%3ATools%3A%3ARun%3A%3AAlignment%3A%3AMuscle)\n\n    use Env qw(@PATH);\n    use Bio::Tools::Run::Alignment::Muscle;\n    unshift @PATH, Alien::MUSCLE-\u003ebin_dir;\n    $muscle = Bio::Tools::Run::Alignment::Muscle-\u003enew(@params);\n    $align = $muscle-\u003ealign('sequences.fa');\n\n# DESCRIPTION\n\nDiscover or download and install [MUSCLE](https://www.drive5.com/muscle/).\n\n# METHODS\n\n[Alien::MUSCLE](https://metacpan.org/pod/Alien%3A%3AMUSCLE) inherits all the methods from [Alien::Base](https://metacpan.org/pod/Alien%3A%3ABase) and implements the\nfollowing new ones.\n\n## muscle\\_binary\n\n    # \"/installed/path/to/muscle\"\n    $binary = Alien::MUSCLE-\u003emuscle_binary;\n\nThe full path to the installed muscle.\n\n## muscle\\_dist\\_type\n\n    # \"source\"\n    $type = Alien::MUSCLE-\u003emuscle_dist_type;\n\nHow the program was installed. This is either _source_, if the source\ndistribution was downloaded and built, or _binary_ if the pre-built software\nwas downloaded and installed. The pre-built software is statically compiled.\n\n# INSTALLATION\n\nInstalling [Alien::MUSCLE](https://metacpan.org/pod/Alien%3A%3AMUSCLE) is straight forward.\n\nIf you have [cpanm](https://metacpan.org/pod/cpanm), you only need one line:\n\n    cpanm Alien::MUSCLE\n\nOtherwise, any other cpan client may be used.\n\n## INFLUENTIAL ENVIRONMENT VARIABLES\n\nInstallation may be customised to a limited extent with the following\nenvironment variables:\n\n- ALIEN\\_MUSCLE\\_FORCE\\_BINARY\n\n    Setting this variable to a true value will force the download of a pre-built\n    binary distribution of [MUSCLE](https://www.drive5.com/muscle/). These versions\n    are statically compiled and will not require a compiler on the local machine.\n    However there are a limited number of architectures provided and a source\n    install may be better in those situations.\n\n# COPYRIGHT \u0026 LICENSE\n\nThis library is free software. You can redistribute it and/or modify it under\nthe same terms as Perl itself.\n\n# AUTHORS\n\nRoy Storey - \u003ckiwiroy@cpan.org\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkiwiroy%2Fp5-alien-muscle","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkiwiroy%2Fp5-alien-muscle","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkiwiroy%2Fp5-alien-muscle/lists"}