From owner-svn-ports-all@freebsd.org Wed Jun 6 15:15:20 2018 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 3FA39FD0BBE; Wed, 6 Jun 2018 15:15:20 +0000 (UTC) (envelope-from krion@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id DBD3A7918E; Wed, 6 Jun 2018 15:15:19 +0000 (UTC) (envelope-from krion@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 B8D564B69; Wed, 6 Jun 2018 15:15:19 +0000 (UTC) (envelope-from krion@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id w56FFJJC061363; Wed, 6 Jun 2018 15:15:19 GMT (envelope-from krion@FreeBSD.org) Received: (from krion@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id w56FFI0k061356; Wed, 6 Jun 2018 15:15:18 GMT (envelope-from krion@FreeBSD.org) Message-Id: <201806061515.w56FFI0k061356@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: krion set sender to krion@FreeBSD.org using -f From: Kirill Ponomarev Date: Wed, 6 Jun 2018 15:15:18 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r471850 - in head/biology: . infernal infernal/files X-SVN-Group: ports-head X-SVN-Commit-Author: krion X-SVN-Commit-Paths: in head/biology: . infernal infernal/files X-SVN-Commit-Revision: 471850 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: 2.1.26 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: Wed, 06 Jun 2018 15:15:20 -0000 Author: krion Date: Wed Jun 6 15:15:18 2018 New Revision: 471850 URL: https://svnweb.freebsd.org/changeset/ports/471850 Log: Add new port: biology/infernal Infernal is a tool for searching DNA sequence database for RNA structure and sequence similarities. The Rfam database of RNA families is based on Infernal, and we can search DNA sequences for structural homologs of Rfam families. WWW: http://eddylab.org/infernal/ PR: 228776 Submitted by: Motomichi Matsuzaki Added: head/biology/infernal/ head/biology/infernal/Makefile (contents, props changed) head/biology/infernal/distinfo (contents, props changed) head/biology/infernal/files/ head/biology/infernal/files/patch-configure (contents, props changed) head/biology/infernal/pkg-descr (contents, props changed) head/biology/infernal/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Wed Jun 6 15:13:12 2018 (r471849) +++ head/biology/Makefile Wed Jun 6 15:15:18 2018 (r471850) @@ -45,6 +45,7 @@ SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy + SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview Added: head/biology/infernal/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/infernal/Makefile Wed Jun 6 15:15:18 2018 (r471850) @@ -0,0 +1,46 @@ +# $FreeBSD$ + +PORTNAME= infernal +PORTVERSION= 1.1.2 +CATEGORIES= biology +MASTER_SITES= http://eddylab.org/infernal/ + +MAINTAINER= mzaki@niid.go.jp +COMMENT= Search sequence databases for structural RNA homologs + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +ONLY_FOR_ARCHS= amd64 i386 +ONLY_FOR_ARCHS_REASON= requires SSE2 or AltiVec instructions + +USES= gmake +GNU_CONFIGURE= yes +MAKE_ARGS= V=1 + +DOCFILES= Userguide.pdf +EXAMPLES= 5S_rRNA.c.cm 5S_rRNA.sto \ + Cobalamin.c.cm Cobalamin.fa Cobalamin.sto \ + metag-example.fa minifam-metag.out minifam.cm \ + minifam.cm.i1f minifam.cm.i1i minifam.cm.i1m minifam.cm.i1p \ + mrum-genome.fa mrum-tRNAs10.fa mrum-tRNAs10.out \ + tRNA5-hand.c.cm tRNA5-hand.sto tRNA5-mrum.out \ + tRNA5-noss.sto tRNA5.c.cm tRNA5.sto + +OPTIONS_DEFINE= DOCS EXAMPLES TEST + +TEST_TEST_TARGET= check +TEST_USES= shebangfix perl5 +TEST_VARS= shebang_glob=*.pl shebang_files=easel/devkit/* use_perl5=build + +post-build-TEST-on: do-test + +post-install-DOCS-on: + @${MKDIR} ${STAGEDIR}${DOCSDIR} + ${INSTALL_DATA} ${DOCFILES:S,^,${WRKSRC}/,} ${STAGEDIR}${DOCSDIR} + +post-install-EXAMPLES-on: + @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} + ${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/tutorial/,} ${STAGEDIR}${EXAMPLESDIR} + +.include Added: head/biology/infernal/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/infernal/distinfo Wed Jun 6 15:15:18 2018 (r471850) @@ -0,0 +1,3 @@ +TIMESTAMP = 1528251928 +SHA256 (infernal-1.1.2.tar.gz) = ac8c24f484205cfb7124c38d6dc638a28f2b9035b9433efec5dc753c7e84226b +SIZE (infernal-1.1.2.tar.gz) = 19364073 Added: head/biology/infernal/files/patch-configure ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/infernal/files/patch-configure Wed Jun 6 15:15:18 2018 (r471850) @@ -0,0 +1,10 @@ +--- configure.orig 2016-07-01 20:26:34 UTC ++++ configure +@@ -3855,6 +3855,7 @@ fi + if test "$impl_choice" = "none"; then + case $host in + ia64-*-*) impl_choice=sse;; ++ amd64-*-*) impl_choice=sse;; + i?86-*-*) impl_choice=sse;; + x86*-*-*) impl_choice=sse;; + powerpc*-*-*) impl_choice=vmx;; Added: head/biology/infernal/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/infernal/pkg-descr Wed Jun 6 15:15:18 2018 (r471850) @@ -0,0 +1,14 @@ +Infernal, standing for "INFERence of RNA ALignment", is a tool for searching +DNA sequence database for RNA structure and sequence similarities. + +It is based on Covariance Model (CM), which scores a combination of sequence +consensus and RNA secondary structure consensus, and thus is more capable of +identifying RNA homologs than using primary sequence profile. + +The Rfam database of RNA families is based on Infernal. + +Citation: +Nawrocki & Eddy (2013) Infernal 1.1: 100-fold faster RNA homology searches, +Bioinformatics 29: 2933-2935. + +WWW: http://eddylab.org/infernal/ Added: head/biology/infernal/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/infernal/pkg-plist Wed Jun 6 15:15:18 2018 (r471850) @@ -0,0 +1,43 @@ +bin/cmalign +bin/cmbuild +bin/cmcalibrate +bin/cmconvert +bin/cmemit +bin/cmfetch +bin/cmpress +bin/cmscan +bin/cmsearch +bin/cmstat +man/man1/cmalign.1.gz +man/man1/cmbuild.1.gz +man/man1/cmcalibrate.1.gz +man/man1/cmconvert.1.gz +man/man1/cmemit.1.gz +man/man1/cmfetch.1.gz +man/man1/cmpress.1.gz +man/man1/cmscan.1.gz +man/man1/cmsearch.1.gz +man/man1/cmstat.1.gz +man/man1/infernal.1.gz +%%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/5S_rRNA.c.cm +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/5S_rRNA.sto +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Cobalamin.c.cm +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Cobalamin.fa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Cobalamin.sto +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/metag-example.fa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam-metag.out +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm.i1f +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm.i1i +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm.i1m +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm.i1p +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mrum-genome.fa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mrum-tRNAs10.fa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mrum-tRNAs10.out +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-hand.c.cm +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-hand.sto +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-mrum.out +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-noss.sto +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5.c.cm +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5.sto