svn commit: r471852 - in head/biology/tRNAscan-SE: . files
Kirill Ponomarev
krion at FreeBSD.org
Wed Jun 6 15:20:59 UTC 2018
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 at 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 at FreeBSD.org
-COMMENT= Improved tool for transfer RNA detection
+MAINTAINER= mzaki at 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 at soe.ucsc.edu])
++AC_INIT([tRNAscan-SE],[2.0.0],[pchan at 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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