Date: Wed, 6 Jun 2018 15:15:18 +0000 (UTC) From: Kirill Ponomarev <krion@FreeBSD.org> 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 Message-ID: <201806061515.w56FFI0k061356@repo.freebsd.org>
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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 <mzaki@niid.go.jp> 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 <bsd.port.mk> 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
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