Attachment #237212 for bug #266966

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PORTNAME=	tRNAscan-SE
PORTVERSION=	2.0.11
CATEGORIES=	biology
MASTER_SITES=	http://trna.ucsc.edu/software/
DISTFILES=	${DISTNAME:tl}${EXTRACT_SUFX}


USES=		perl5 autoreconf

WRKSRC=		${WRKDIR}/${DISTNAME:C,\.[0-9]+$,,}

GNU_CONFIGURE=	yes

MAKE_JOBS_UNSAFE=	yes

WRKSRC=		${WRKDIR}/${DISTNAME:C,\.[0-9]+$,,}

.include <bsd.port.mk>

Lines 1-3 Link Here

(-)b/biology/tRNAscan-SE/distinfo (-3 / +3 lines)
1	TIMESTAMP = 1578666520	1	TIMESTAMP = 1665480264
2	SHA256 (trnascan-se-2.0.5.tar.gz) = 92917c2dbec31f9cebef88671418696f077768f00fb7fe483be1a6093b4e7e60	2	SHA256 (trnascan-se-2.0.11.tar.gz) = 29b74edd0f84ad88139035e119b66397c54a37428e0b61c66a1b3d4733adcd1e
3	SIZE (trnascan-se-2.0.5.tar.gz) = 4373181	3	SIZE (trnascan-se-2.0.11.tar.gz) = 4430973




bin/EukHighConfidenceFilter
bin/MitoHighConfidenceFilter
bin/covels-SE
bin/coves-SE
bin/eufindtRNA

%%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

%%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

%%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
- 

Return to bug 266966

Lines 1-5 Link Here

(-)b/biology/tRNAscan-SE/Makefile (-3 / +3 lines)
1	PORTNAME= tRNAscan-SE	1	PORTNAME= tRNAscan-SE
2	PORTVERSION= 2.0.5	2	PORTVERSION= 2.0.11
3	CATEGORIES= biology	3	CATEGORIES= biology
4	MASTER_SITES= http://trna.ucsc.edu/software/	4	MASTER_SITES= http://trna.ucsc.edu/software/
5	DISTFILES= ${DISTNAME:tl}${EXTRACT_SUFX}	5	DISTFILES= ${DISTNAME:tl}${EXTRACT_SUFX}
Lines 15-24 RUN_DEPENDS= cmsearch:biology/infernal Link Here
15		15
16	USES= perl5 autoreconf	16	USES= perl5 autoreconf
17		17
18	WRKSRC= ${WRKDIR}/${DISTNAME:C,\.[0-9]+$,,}
19
20	GNU_CONFIGURE= yes	18	GNU_CONFIGURE= yes
21		19
22	MAKE_JOBS_UNSAFE= yes	20	MAKE_JOBS_UNSAFE= yes
23		21
		22	WRKSRC= ${WRKDIR}/${DISTNAME:C,\.[0-9]+$,,}
		23
24	.include <bsd.port.mk>	24	.include <bsd.port.mk>

Lines 22-29 Link Here

(-)b/biology/tRNAscan-SE/files/patch-Makefile.am (-3 / +3 lines)
22		22
23	# process scripts	23	# process scripts
24	# treat tRNAscan-SE.conf as a script since it's just easier	24	# treat tRNAscan-SE.conf as a script since it's just easier
25	-dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter tRNAscan-SE tRNAscan-SE.conf	25	-dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter bin/MitoHighConfidenceFilter tRNAscan-SE tRNAscan-SE.conf
26	+dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter tRNAscan-SE	26	+dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter bin/MitoHighConfidenceFilter tRNAscan-SE
27	+sysconf_DATA = tRNAscan-SE.conf	27	+sysconf_DATA = tRNAscan-SE.conf
28	# for a few files, need to substitute perl path, bin directory, and lib directory	28	# for a few files, need to substitute perl path, bin directory, and lib directory
29	# first, define a function for it	29	# first, define a function for it
Lines 34-40 Link Here
34	CLEANFILES = $(dist_bin_SCRIPTS) $(srcdir)/lib/*	34	CLEANFILES = $(dist_bin_SCRIPTS) $(srcdir)/lib/*
35	-include_HEADERS = $(srcdir)/src/*.h	35	-include_HEADERS = $(srcdir)/src/*.h
36	+#include_HEADERS = $(srcdir)/src/*.h	36	+#include_HEADERS = $(srcdir)/src/*.h
37	EXTRA_DIST = lib src/sstofa.in src/fasta2gsi.in EukHighConfidenceFilter tRNAscan-SE.src tRNAscan-SE.conf.src	37	EXTRA_DIST = lib src/sstofa.in src/fasta2gsi.in EukHighConfidenceFilter MitoHighConfidenceFilter tRNAscan-SE.src tRNAscan-SE.conf.src
38		38
39	# then create build rules	39	# then create build rules
40	@@ -61,16 +62,9 @@ bin/EukHighConfidenceFilter: EukHighConf	40	@@ -61,16 +62,9 @@ bin/EukHighConfidenceFilter: EukHighConf

Lines 1-4 Link Here

(-)b/biology/tRNAscan-SE/pkg-plist (-1 / +4 lines)
1	bin/EukHighConfidenceFilter	1	bin/EukHighConfidenceFilter
		2	bin/MitoHighConfidenceFilter
2	bin/covels-SE	3	bin/covels-SE
3	bin/coves-SE	4	bin/coves-SE
4	bin/eufindtRNA	5	bin/eufindtRNA
Lines 10-15 etc/tRNAscan-SE.conf Link Here
10	%%DATADIR%%/gcode/gcode.cilnuc	11	%%DATADIR%%/gcode/gcode.cilnuc
11	%%DATADIR%%/gcode/gcode.echdmito	12	%%DATADIR%%/gcode/gcode.echdmito
12	%%DATADIR%%/gcode/gcode.invmito	13	%%DATADIR%%/gcode/gcode.invmito
		14	%%DATADIR%%/gcode/gcode.marsumito
13	%%DATADIR%%/gcode/gcode.othmito	15	%%DATADIR%%/gcode/gcode.othmito
14	%%DATADIR%%/gcode/gcode.vertmito	16	%%DATADIR%%/gcode/gcode.vertmito
15	%%DATADIR%%/gcode/gcode.ystmito	17	%%DATADIR%%/gcode/gcode.ystmito
Lines 86-91 etc/tRNAscan-SE.conf Link Here
86	%%DATADIR%%/models/TRNAinf-mito-vert-Arg.cm	88	%%DATADIR%%/models/TRNAinf-mito-vert-Arg.cm
87	%%DATADIR%%/models/TRNAinf-mito-vert-Asn.cm	89	%%DATADIR%%/models/TRNAinf-mito-vert-Asn.cm
88	%%DATADIR%%/models/TRNAinf-mito-vert-Asp.cm	90	%%DATADIR%%/models/TRNAinf-mito-vert-Asp.cm
		91	%%DATADIR%%/models/TRNAinf-mito-vert-Cys-no-darm.cm
89	%%DATADIR%%/models/TRNAinf-mito-vert-Cys.cm	92	%%DATADIR%%/models/TRNAinf-mito-vert-Cys.cm
90	%%DATADIR%%/models/TRNAinf-mito-vert-Gln.cm	93	%%DATADIR%%/models/TRNAinf-mito-vert-Gln.cm
91	%%DATADIR%%/models/TRNAinf-mito-vert-Glu.cm	94	%%DATADIR%%/models/TRNAinf-mito-vert-Glu.cm
Lines 116-121 etc/tRNAscan-SE.conf Link Here
116	%%DATADIR%%/tRNAscanSE/CM.pm	119	%%DATADIR%%/tRNAscanSE/CM.pm
117	%%DATADIR%%/tRNAscanSE/CMscanResultFile.pm	120	%%DATADIR%%/tRNAscanSE/CMscanResultFile.pm
118	%%DATADIR%%/tRNAscanSE/Configuration.pm	121	%%DATADIR%%/tRNAscanSE/Configuration.pm
		122	%%DATADIR%%/tRNAscanSE/Constants.pm
119	%%DATADIR%%/tRNAscanSE/Eufind.pm	123	%%DATADIR%%/tRNAscanSE/Eufind.pm
120	%%DATADIR%%/tRNAscanSE/FpScanResultFile.pm	124	%%DATADIR%%/tRNAscanSE/FpScanResultFile.pm
121	%%DATADIR%%/tRNAscanSE/GeneticCode.pm	125	%%DATADIR%%/tRNAscanSE/GeneticCode.pm
122	-