From owner-svn-ports-all@freebsd.org Fri Jul 24 07:08:01 2020 Return-Path: Delivered-To: svn-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 6987D37230C; Fri, 24 Jul 2020 07:08:01 +0000 (UTC) (envelope-from sunpoet@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4BCgJd2G76z3WT5; Fri, 24 Jul 2020 07:08:01 +0000 (UTC) (envelope-from sunpoet@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 3028025FF3; Fri, 24 Jul 2020 07:08:01 +0000 (UTC) (envelope-from sunpoet@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 06O781SE041577; Fri, 24 Jul 2020 07:08:01 GMT (envelope-from sunpoet@FreeBSD.org) Received: (from sunpoet@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 06O780Dn041574; Fri, 24 Jul 2020 07:08:00 GMT (envelope-from sunpoet@FreeBSD.org) Message-Id: <202007240708.06O780Dn041574@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: sunpoet set sender to sunpoet@FreeBSD.org using -f From: Sunpoet Po-Chuan Hsieh Date: Fri, 24 Jul 2020 07:08:00 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r543010 - in head/biology: . rubygem-bio-executables X-SVN-Group: ports-head X-SVN-Commit-Author: sunpoet X-SVN-Commit-Paths: in head/biology: . rubygem-bio-executables X-SVN-Commit-Revision: 543010 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.33 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 24 Jul 2020 07:08:01 -0000 Author: sunpoet Date: Fri Jul 24 07:08:00 2020 New Revision: 543010 URL: https://svnweb.freebsd.org/changeset/ports/543010 Log: Add rubygem-bio-executables 1.0.0 bio-executables is a collection of miscellaneous utilities for bioinformatics that were formerly part of the BioRuby core ("bio" gem). Because of reducing complexity, they were moved to this gem. This code has historically been part of the BioRuby gem, but has been split into its own gem as part of an effort to modularize BioRuby. bio-executables and many more plugins are available at biogems.info. WWW: https://github.com/bioruby/bioruby-executables Added: head/biology/rubygem-bio-executables/ head/biology/rubygem-bio-executables/Makefile (contents, props changed) head/biology/rubygem-bio-executables/distinfo (contents, props changed) head/biology/rubygem-bio-executables/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Fri Jul 24 07:07:54 2020 (r543009) +++ head/biology/Makefile Fri Jul 24 07:08:00 2020 (r543010) @@ -148,6 +148,7 @@ SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio + SUBDIR += rubygem-bio-executables SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview Added: head/biology/rubygem-bio-executables/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/rubygem-bio-executables/Makefile Fri Jul 24 07:08:00 2020 (r543010) @@ -0,0 +1,30 @@ +# Created by: Po-Chuan Hsieh +# $FreeBSD$ + +PORTNAME= bio-executables +PORTVERSION= 1.0.0 +CATEGORIES= biology rubygems +MASTER_SITES= RG + +MAINTAINER= sunpoet@FreeBSD.org +COMMENT= Collection of miscellaneous utilities for bioinformatics + +LICENSE= BSD2CLAUSE RUBY +LICENSE_COMB= dual +LICENSE_FILE_BSD2CLAUSE=${WRKSRC}/BSDL +LICENSE_FILE_RUBY= ${WRKSRC}/COPYING + +RUN_DEPENDS= rubygem-bio>=2.0.0:biology/rubygem-bio \ + rubygem-bio-old-biofetch-emulator>=0.0.1:biology/rubygem-bio-old-biofetch-emulator + +USES= gem +USE_RUBY= yes + +NO_ARCH= yes + +PLIST_FILES= bin/br_biofetch.rb \ + bin/br_bioflat.rb \ + bin/br_biogetseq.rb \ + bin/br_pmfetch.rb + +.include Added: head/biology/rubygem-bio-executables/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/rubygem-bio-executables/distinfo Fri Jul 24 07:08:00 2020 (r543010) @@ -0,0 +1,3 @@ +TIMESTAMP = 1595416507 +SHA256 (rubygem/bio-executables-1.0.0.gem) = 29f02115bc543d7f39b0c6d4c518719dcae9d112a913c215b988b599a6736b91 +SIZE (rubygem/bio-executables-1.0.0.gem) = 15360 Added: head/biology/rubygem-bio-executables/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/rubygem-bio-executables/pkg-descr Fri Jul 24 07:08:00 2020 (r543010) @@ -0,0 +1,9 @@ +bio-executables is a collection of miscellaneous utilities for bioinformatics +that were formerly part of the BioRuby core ("bio" gem). Because of reducing +complexity, they were moved to this gem. + +This code has historically been part of the BioRuby gem, but has been split into +its own gem as part of an effort to modularize BioRuby. bio-executables and many +more plugins are available at biogems.info. + +WWW: https://github.com/bioruby/bioruby-executables