From owner-svn-ports-head@freebsd.org Fri May 15 04:58:28 2020 Return-Path: Delivered-To: svn-ports-head@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 EC87F2E9F47; Fri, 15 May 2020 04:58:28 +0000 (UTC) (envelope-from yuri@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) server-signature RSA-PSS (4096 bits) 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 49NblS63BWz4Ly3; Fri, 15 May 2020 04:58:28 +0000 (UTC) (envelope-from yuri@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 C683F1EDE1; Fri, 15 May 2020 04:58:28 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 04F4wS0R092133; Fri, 15 May 2020 04:58:28 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 04F4wRkD092128; Fri, 15 May 2020 04:58:27 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <202005150458.04F4wRkD092128@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Fri, 15 May 2020 04:58:27 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r535266 - in head/biology: . scrm scrm/files X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology: . scrm scrm/files X-SVN-Commit-Revision: 535266 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.33 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 15 May 2020 04:58:29 -0000 Author: yuri Date: Fri May 15 04:58:27 2020 New Revision: 535266 URL: https://svnweb.freebsd.org/changeset/ports/535266 Log: New port: biology/scrm: Coalescent simulator for biological sequences Added: head/biology/scrm/ head/biology/scrm/Makefile (contents, props changed) head/biology/scrm/distinfo (contents, props changed) head/biology/scrm/files/ head/biology/scrm/files/patch-src_random_fastfunc.h (contents, props changed) head/biology/scrm/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Fri May 15 04:25:56 2020 (r535265) +++ head/biology/Makefile Fri May 15 04:58:27 2020 (r535266) @@ -143,6 +143,7 @@ SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools + SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps Added: head/biology/scrm/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/scrm/Makefile Fri May 15 04:58:27 2020 (r535266) @@ -0,0 +1,22 @@ +# $FreeBSD$ + +PORTNAME= scrm +DISTVERSIONPREFIX= v +DISTVERSION= 1.7.4 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Coalescent simulator for biological sequences + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/COPYING + +USES= autoreconf gmake +USE_GITHUB= yes + +GNU_CONFIGURE= yes + +PLIST_FILES= bin/scrm \ + man/man1/scrm.1.gz + +.include Added: head/biology/scrm/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/scrm/distinfo Fri May 15 04:58:27 2020 (r535266) @@ -0,0 +1,3 @@ +TIMESTAMP = 1589518122 +SHA256 (scrm-scrm-v1.7.4_GH0.tar.gz) = 13f4b0febabcdf6a2b478693febd2fb9d3f47532fb39ffaa4f01fe816f69ceb7 +SIZE (scrm-scrm-v1.7.4_GH0.tar.gz) = 341612 Added: head/biology/scrm/files/patch-src_random_fastfunc.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/scrm/files/patch-src_random_fastfunc.h Fri May 15 04:58:27 2020 (r535266) @@ -0,0 +1,11 @@ +--- src/random/fastfunc.h.orig 2020-05-15 04:49:19 UTC ++++ src/random/fastfunc.h +@@ -27,7 +27,7 @@ + #include + #include + +-#if !defined(__APPLE__) ++#if !defined(__APPLE__) && !defined(__FreeBSD__) + #include + #endif + Added: head/biology/scrm/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/scrm/pkg-descr Fri May 15 04:58:27 2020 (r535266) @@ -0,0 +1,8 @@ +scrm simulates the evolution of genetic sequences. It takes a neutral +evolutionary model as input, and generates random sequences that evolved under +the model. As coalescent simulator, it traces the ancestry of the sampled +sequences backwards in time and is therefore extremely efficient. Compared to +other coalescent simulators, it can simulate chromosome-scale sequences without +a measureable reduction of genetic linkage between different sites. + +WWW: https://scrm.github.io/