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biology/tRNAscan-SE: Update to 2.0.11 

ChangeLog:	http://lowelab.ucsc.edu/tRNAscan-SE/change_log.txt
PR:		266966
2023Q1
Motomichi Matsuzaki 2022-10-12 12:43:51 +01:00 committed by Nuno Teixeira
parent 010ed26540
commit 5a4350de94
4 changed files with 14 additions and 10 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
biology/tRNAscan-SE/Makefile
View File

@ -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>

6
biology/tRNAscan-SE/distinfo
View File

@ -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

6
biology/tRNAscan-SE/files/patch-Makefile.am
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@ -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

4
biology/tRNAscan-SE/pkg-plist
View File

@ -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