Date: Wed, 6 Jun 2018 15:20:57 +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: r471852 - in head/biology/tRNAscan-SE: . files Message-ID: <201806061520.w56FKvHo064137@repo.freebsd.org>
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Author: krion Date: Wed Jun 6 15:20:57 2018 New Revision: 471852 URL: https://svnweb.freebsd.org/changeset/ports/471852 Log: Update to 2.0.0 and pass maintainership to committer. PR: 228758 Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp> Added: head/biology/tRNAscan-SE/files/patch-Makefile.am (contents, props changed) head/biology/tRNAscan-SE/files/patch-configure.ac (contents, props changed) head/biology/tRNAscan-SE/files/patch-tRNAscan-SE.src (contents, props changed) Deleted: head/biology/tRNAscan-SE/files/patch-Makefile head/biology/tRNAscan-SE/files/patch-sqio.c Modified: head/biology/tRNAscan-SE/Makefile head/biology/tRNAscan-SE/distinfo head/biology/tRNAscan-SE/pkg-descr Modified: head/biology/tRNAscan-SE/Makefile ============================================================================== --- head/biology/tRNAscan-SE/Makefile Wed Jun 6 15:17:12 2018 (r471851) +++ head/biology/tRNAscan-SE/Makefile Wed Jun 6 15:20:57 2018 (r471852) @@ -2,46 +2,23 @@ # $FreeBSD$ PORTNAME= tRNAscan-SE -PORTVERSION= 1.23 -PORTREVISION= 1 +PORTVERSION= 2.0.0 CATEGORIES= biology -MASTER_SITES= ftp://selab.janelia.org/pub/software/tRNAscan-SE/ +MASTER_SITES= http://lowelab.ucsc.edu/software/ +DISTFILES= ${DISTNAME:tl}${EXTRACT_SUFX} -MAINTAINER= ports@FreeBSD.org -COMMENT= Improved tool for transfer RNA detection +MAINTAINER= mzaki@niid.go.jp +COMMENT= Searching for tRNA genes in genomic sequence -BROKEN= No public distfiles -DEPRECATED= Broken for more than 6 months -EXPIRATION_DATE= 2018-06-06 +LICENSE= GPLv3+ +LICENSE_FILE= ${WRKSRC}/COPYING -USES= perl5 tar:Z -MAKE_ARGS= BINDIR="${PREFIX}/bin" \ - LIBDIR="${DATADIR}" \ - CC="${CC}" \ - CFLAGS="${CFLAGS}" +RUN_DEPENDS= cmsearch:biology/infernal -PLIST_FILES+= bin/covels-SE bin/coves-SE bin/eufindtRNA bin/tRNAscan-SE bin/trnascan-1.4 \ - man/man1/tRNAscan-SE.1.gz -PORTDATA= * -PORTDOCS= Manual.ps +WRKSRC= ${WRKDIR}/${DISTNAME:S,.0$,,} -OPTIONS_DEFINE= DOCS +GNU_CONFIGURE= yes -post-patch: - @${REINPLACE_CMD} -e 's|tRNAscanSE setpaths|tRNAscanSE|g ; \ - s|if tRNAscan-SE|if ./tRNAscan-SE|g' ${WRKSRC}/Makefile - -do-install: -.for f in covels-SE coves-SE eufindtRNA trnascan-1.4 - ${INSTALL_PROGRAM} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin -.endfor - ${INSTALL_SCRIPT} ${WRKSRC}/tRNAscan-SE ${STAGEDIR}${PREFIX}/bin - ${INSTALL_MAN} ${WRKSRC}/tRNAscan-SE.man ${STAGEDIR}${MANPREFIX}/man/man1/tRNAscan-SE.1 - @${MKDIR} ${STAGEDIR}${DATADIR} -.for f in TPCsignal Dsignal *.cm gcode.* - ${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DATADIR} -.endfor - @${MKDIR} ${STAGEDIR}${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/Manual.ps ${STAGEDIR}${DOCSDIR} +USES= perl5 autoreconf .include <bsd.port.mk> Modified: head/biology/tRNAscan-SE/distinfo ============================================================================== --- head/biology/tRNAscan-SE/distinfo Wed Jun 6 15:17:12 2018 (r471851) +++ head/biology/tRNAscan-SE/distinfo Wed Jun 6 15:20:57 2018 (r471852) @@ -1,2 +1,3 @@ -SHA256 (tRNAscan-SE-1.23.tar.Z) = 843caf3e258a6293300513ddca7eb7dbbd2225e5baae1e5a7bcafd509f6dd550 -SIZE (tRNAscan-SE-1.23.tar.Z) = 846349 +TIMESTAMP = 1528270436 +SHA256 (trnascan-se-2.0.0.tar.gz) = 0dde1c07142e4bf77b21d53ddf3eeb1ef8c52248005a42323d13f8d7c798100c +SIZE (trnascan-se-2.0.0.tar.gz) = 4372755 Added: head/biology/tRNAscan-SE/files/patch-Makefile.am ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tRNAscan-SE/files/patch-Makefile.am Wed Jun 6 15:20:57 2018 (r471852) @@ -0,0 +1,62 @@ +--- Makefile.am.orig 2017-12-03 07:00:58 UTC ++++ Makefile.am +@@ -8,8 +8,8 @@ + AUTOMAKE_OPTIONS = foreign subdir-objects + + # set flags +-AM_CFLAGS = -O +-LDADD = -lm ++#AM_CFLAGS = -O ++#LDADD = -lm + + # macros for program dependencies + EUFIND = src/eufind_const.h src/eufind_main.c src/pavesi.c +@@ -23,20 +23,21 @@ COVESRC = src/align.c src/dbviterbi.c sr + bin_PROGRAMS = bin/eufindtRNA bin/trnascan-1.4 bin/covels-SE bin/coves-SE + bin_eufindtRNA_SOURCES = $(SQUIDHDRS) $(SQUIDSRC) $(EUFIND) + bin_trnascan_1_4_SOURCES = src/trnascan.c +-bin_trnascan_1_4_CFLAGS = -DTSCANDIR=\"$(libdir)\/tRNAscan-SE\/models\" $(AM_CFLAGS) ++bin_trnascan_1_4_CFLAGS = -DTSCANDIR=\"$(datadir)\/tRNAscan-SE\/models\" $(AM_CFLAGS) + bin_covels_SE_SOURCES = $(COVESRC) src/scan_main.c + bin_coves_SE_SOURCES = $(COVESRC) src/score_main.c + + # process scripts + # treat tRNAscan-SE.conf as a script since it's just easier +-dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter tRNAscan-SE tRNAscan-SE.conf ++dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter tRNAscan-SE ++sysconf_DATA = tRNAscan-SE.conf + # for a few files, need to substitute perl path, bin directory, and lib directory + # first, define a function for it +-do_subst = sed -e 's,\@bindir\@,$(bindir),g' -e 's,\@libdir\@,$(libdir),g' -e 's,[@]PERL[@],$(PERL),g' -e 's,\@INFERNAL\@,$(INFERNAL),g' ++do_subst = sed -e 's,\@bindir\@,$(bindir),g' -e 's,\@libdir\@,$(datadir),g' -e 's,\@sysconfdir\@,$(sysconfdir),g' -e 's,[@]PERL[@],$(PERL),g' -e 's,\@INFERNAL\@,$(INFERNAL),g' + + # extra steps for cleaning/distribution + CLEANFILES = $(dist_bin_SCRIPTS) $(srcdir)/lib/* +-include_HEADERS = $(srcdir)/src/*.h ++#include_HEADERS = $(srcdir)/src/*.h + EXTRA_DIST = lib src/sstofa.in src/fasta2gsi.in EukHighConfidenceFilter tRNAscan-SE.src tRNAscan-SE.conf.src + + # then create build rules +@@ -61,16 +62,9 @@ bin/EukHighConfidenceFilter: EukHighConf + $(do_subst) < $(srcdir)/EukHighConfidenceFilter.in > bin/EukHighConfidenceFilter + chmod +x bin/EukHighConfidenceFilter + +-# copy libraries. We don't have "libraries" in the libgmp.so.4 kind, but we do have data libraries, so we don't have to deal with lib_LTLIBRARIES. +-install-data-hook: +- chmod u+w $(exec_prefix) +- test -d $(libdir) || mkdir $(libdir) +- chmod u+w $(libdir) +- test -d $(libdir)/tRNAscan-SE || mkdir $(libdir)/tRNAscan-SE +- cp -rf $(srcdir)/lib/* $(libdir)/tRNAscan-SE +- +-# remove lib/ files during uninstallation. A bit of a hack, since lib files are write-protected by default. Files +-uninstall-hook: +- chmod -R u+w $(libdir)/tRNAscan-SE +- rm -rf $(libdir)/tRNAscan-SE +- ++gcodedir = $(pkgdatadir)/gcode ++modelsdir = $(pkgdatadir)/models ++modulesdir = $(pkgdatadir)/tRNAscanSE ++dist_gcode_DATA = lib/gcode/* ++dist_models_DATA = lib/models/* ++dist_modules_DATA = lib/tRNAscanSE/* Added: head/biology/tRNAscan-SE/files/patch-configure.ac ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tRNAscan-SE/files/patch-configure.ac Wed Jun 6 15:20:57 2018 (r471852) @@ -0,0 +1,21 @@ +--- configure.ac.orig 2017-04-27 20:18:19 UTC ++++ configure.ac +@@ -4,7 +4,7 @@ + ## Settings for generating a configure file + + AC_PREREQ([2.69]) +-AC_INIT([tRNAscan-SE],[2.0.0],[pchan@soe.ucsc.edu]) ++AC_INIT([tRNAscan-SE],[2.0.0],[pchan@soe.ucsc.edu],[tRNAscan-SE]) + AC_CONFIG_HEADERS([config.h]) + + # Checks for programs. +@@ -33,7 +33,8 @@ AC_TYPE_SIZE_T + # Checks for library functions. + AC_FUNC_MALLOC + AC_FUNC_REALLOC +-AC_CHECK_FUNCS([bzero memset re_comp regcomp sqrt strcasecmp strchr strstr]) ++AC_CHECK_FUNCS([bzero memset re_comp regcomp strcasecmp strchr strstr]) ++AC_SEARCH_LIBS([sqrt],[m]) + + # use automake + AM_INIT_AUTOMAKE([foreign]) Added: head/biology/tRNAscan-SE/files/patch-tRNAscan-SE.src ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tRNAscan-SE/files/patch-tRNAscan-SE.src Wed Jun 6 15:20:57 2018 (r471852) @@ -0,0 +1,17 @@ +--- tRNAscan-SE.src.orig 2017-12-03 01:59:25 UTC ++++ tRNAscan-SE.src +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! @PERL@ + # + # -------------------------------------------------------------------- + # tRNAscan-SE: a program for improved detection of transfer RNA +@@ -44,7 +44,7 @@ our $release_date = "December 2017"; + our $program_id = "tRNAscan-SE-".$version; + + # modified by 'make' +-our $default_conf = "@bindir@/tRNAscan-SE.conf"; ++our $default_conf = "@sysconfdir@/tRNAscan-SE.conf"; + + # Signal handling + $SIG{'TERM'} = 'error_handler'; Modified: head/biology/tRNAscan-SE/pkg-descr ============================================================================== --- head/biology/tRNAscan-SE/pkg-descr Wed Jun 6 15:17:12 2018 (r471851) +++ head/biology/tRNAscan-SE/pkg-descr Wed Jun 6 15:20:57 2018 (r471852) @@ -7,4 +7,4 @@ the flow of information between them, performing a lim post-processing, and outputting the results in one of several formats. -WWW: http://selab.janelia.org/software.html +WWW: http://lowelab.ucsc.edu/tRNAscan-SE/
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