Date: Wed, 12 Oct 2022 11:45:35 GMT From: Nuno Teixeira <eduardo@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 5a4350de941e - main - biology/tRNAscan-SE: Update to 2.0.11 Message-ID: <202210121145.29CBjZen031755@gitrepo.freebsd.org>
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The branch main has been updated by eduardo: URL: https://cgit.FreeBSD.org/ports/commit/?id=5a4350de941e061def79fb2ab6b6f46d5eb10ad9 commit 5a4350de941e061def79fb2ab6b6f46d5eb10ad9 Author: Motomichi Matsuzaki <mzaki@e-mail.ne.jp> AuthorDate: 2022-10-12 11:43:51 +0000 Commit: Nuno Teixeira <eduardo@FreeBSD.org> CommitDate: 2022-10-12 11:45:24 +0000 biology/tRNAscan-SE: Update to 2.0.11 ChangeLog: http://lowelab.ucsc.edu/tRNAscan-SE/change_log.txt PR: 266966 --- biology/tRNAscan-SE/Makefile | 8 ++++---- biology/tRNAscan-SE/distinfo | 6 +++--- biology/tRNAscan-SE/files/patch-Makefile.am | 6 +++--- biology/tRNAscan-SE/pkg-plist | 4 ++++ 4 files changed, 14 insertions(+), 10 deletions(-) diff --git a/biology/tRNAscan-SE/Makefile b/biology/tRNAscan-SE/Makefile index 75658cb534c0..c80daf7fb373 100644 --- a/biology/tRNAscan-SE/Makefile +++ b/biology/tRNAscan-SE/Makefile @@ -1,5 +1,5 @@ PORTNAME= tRNAscan-SE -PORTVERSION= 2.0.5 +PORTVERSION= 2.0.11 CATEGORIES= biology MASTER_SITES= http://trna.ucsc.edu/software/ DISTFILES= ${DISTNAME:tl}${EXTRACT_SUFX} @@ -13,12 +13,12 @@ LICENSE_FILE= ${WRKSRC}/COPYING RUN_DEPENDS= cmsearch:biology/infernal -USES= perl5 autoreconf - -WRKSRC= ${WRKDIR}/${DISTNAME:C,\.[0-9]+$,,} +USES= autoreconf perl5 GNU_CONFIGURE= yes MAKE_JOBS_UNSAFE= yes +WRKSRC= ${WRKDIR}/${DISTNAME:C,\.[0-9]+$,,} + .include <bsd.port.mk> diff --git a/biology/tRNAscan-SE/distinfo b/biology/tRNAscan-SE/distinfo index a57336279094..8adefb253c6a 100644 --- a/biology/tRNAscan-SE/distinfo +++ b/biology/tRNAscan-SE/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1578666520 -SHA256 (trnascan-se-2.0.5.tar.gz) = 92917c2dbec31f9cebef88671418696f077768f00fb7fe483be1a6093b4e7e60 -SIZE (trnascan-se-2.0.5.tar.gz) = 4373181 +TIMESTAMP = 1665480264 +SHA256 (trnascan-se-2.0.11.tar.gz) = 29b74edd0f84ad88139035e119b66397c54a37428e0b61c66a1b3d4733adcd1e +SIZE (trnascan-se-2.0.11.tar.gz) = 4430973 diff --git a/biology/tRNAscan-SE/files/patch-Makefile.am b/biology/tRNAscan-SE/files/patch-Makefile.am index 7a28de19c450..13be4377e71e 100644 --- a/biology/tRNAscan-SE/files/patch-Makefile.am +++ b/biology/tRNAscan-SE/files/patch-Makefile.am @@ -22,8 +22,8 @@ # 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 +-dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter bin/MitoHighConfidenceFilter tRNAscan-SE tRNAscan-SE.conf ++dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter bin/MitoHighConfidenceFilter 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 @@ -34,7 +34,7 @@ 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 + EXTRA_DIST = lib src/sstofa.in src/fasta2gsi.in EukHighConfidenceFilter MitoHighConfidenceFilter tRNAscan-SE.src tRNAscan-SE.conf.src # then create build rules @@ -61,16 +62,9 @@ bin/EukHighConfidenceFilter: EukHighConf diff --git a/biology/tRNAscan-SE/pkg-plist b/biology/tRNAscan-SE/pkg-plist index bb3ebb6f07a9..6dbe93e6916f 100644 --- a/biology/tRNAscan-SE/pkg-plist +++ b/biology/tRNAscan-SE/pkg-plist @@ -1,4 +1,5 @@ bin/EukHighConfidenceFilter +bin/MitoHighConfidenceFilter bin/covels-SE bin/coves-SE bin/eufindtRNA @@ -10,6 +11,7 @@ etc/tRNAscan-SE.conf %%DATADIR%%/gcode/gcode.cilnuc %%DATADIR%%/gcode/gcode.echdmito %%DATADIR%%/gcode/gcode.invmito +%%DATADIR%%/gcode/gcode.marsumito %%DATADIR%%/gcode/gcode.othmito %%DATADIR%%/gcode/gcode.vertmito %%DATADIR%%/gcode/gcode.ystmito @@ -86,6 +88,7 @@ etc/tRNAscan-SE.conf %%DATADIR%%/models/TRNAinf-mito-vert-Arg.cm %%DATADIR%%/models/TRNAinf-mito-vert-Asn.cm %%DATADIR%%/models/TRNAinf-mito-vert-Asp.cm +%%DATADIR%%/models/TRNAinf-mito-vert-Cys-no-darm.cm %%DATADIR%%/models/TRNAinf-mito-vert-Cys.cm %%DATADIR%%/models/TRNAinf-mito-vert-Gln.cm %%DATADIR%%/models/TRNAinf-mito-vert-Glu.cm @@ -116,6 +119,7 @@ etc/tRNAscan-SE.conf %%DATADIR%%/tRNAscanSE/CM.pm %%DATADIR%%/tRNAscanSE/CMscanResultFile.pm %%DATADIR%%/tRNAscanSE/Configuration.pm +%%DATADIR%%/tRNAscanSE/Constants.pm %%DATADIR%%/tRNAscanSE/Eufind.pm %%DATADIR%%/tRNAscanSE/FpScanResultFile.pm %%DATADIR%%/tRNAscanSE/GeneticCode.pm
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