Attachment 194046 Details for Bug 228758 – svn diff (to 2.0.0)

[patch] svn diff (to 2.0.0)

tRNAscan-SE.diff (text/plain), 22.98 KB, created by Motomichi Matsuzaki on 2018-06-06 15:00:54 UTC

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Creator: Motomichi Matsuzaki

Created: 2018-06-06 15:00:54 UTC

Size: 22.98 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 471826)
>+++ Makefile	(working copy)
>@@ -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
>+USES=		perl5 autoreconf
> 
>-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}
>-
> .include <bsd.port.mk>
>Index: distinfo
>===================================================================
>--- distinfo	(revision 471826)
>+++ distinfo	(working copy)
>@@ -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
>Index: files/patch-Makefile
>===================================================================
>--- files/patch-Makefile	(revision 471826)
>+++ files/patch-Makefile	(nonexistent)
>@@ -1,11 +0,0 @@
>---- Makefile.orig	2013-03-17 11:38:57.213776000 +0000
>-+++ Makefile
>-@@ -13,7 +13,7 @@ RFLAGS     = -DRELEASE=$(COV_RELEASE) -D
>- ## greatly speeding scans of unfinished sequence
>- 
>- ## where Perl v.5 (or greater) is installed
>--PERLDIR = /usr/bin
>-+PERLDIR = $(PREFIX)/bin
>- 
>- ## what you call the Perl v.5 executable on your system
>- ## (this could be 'perl5' or otherwise on some systems)
>
>Property changes on: files/patch-Makefile
>___________________________________________________________________
>Deleted: fbsd:nokeywords
>## -1 +0,0 ##
>-yes
>\ No newline at end of property
>Deleted: svn:eol-style
>## -1 +0,0 ##
>-native
>\ No newline at end of property
>Deleted: svn:mime-type
>## -1 +0,0 ##
>-text/plain
>\ No newline at end of property
>Index: files/patch-Makefile.am
>===================================================================
>--- files/patch-Makefile.am	(nonexistent)
>+++ files/patch-Makefile.am	(working copy)
>@@ -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/*
>
>Property changes on: files/patch-Makefile.am
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-configure.ac
>===================================================================
>--- files/patch-configure.ac	(nonexistent)
>+++ files/patch-configure.ac	(working copy)
>@@ -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])
>
>Property changes on: files/patch-configure.ac
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-sqio.c
>===================================================================
>--- files/patch-sqio.c	(revision 471826)
>+++ files/patch-sqio.c	(nonexistent)
>@@ -1,291 +0,0 @@
>---- sqio.c.orig	2002-04-12 20:12:04 UTC
>-+++ sqio.c
>-@@ -235,7 +235,7 @@ readline(FILE *f, char *s)
>- }
>- 
>- static void 
>--getline(struct ReadSeqVars *V)
>-+get_line(struct ReadSeqVars *V)
>- {
>-   readline(V->f, V->sbuffer);
>- }
>-@@ -306,7 +306,7 @@ readLoop(int addfirst, int (*endTest)(ch
>-   V->seqlen = 0;
>-   if (addfirst) addseq(V->sbuffer, V);
>-   do {
>--    getline(V);
>-+    get_line(V);
>-     done = feof(V->f);
>-     done |= (*endTest)(V->sbuffer, &addend);
>-     if (addend || !done)
>-@@ -332,7 +332,7 @@ readPIR(struct ReadSeqVars *V)
>-   char *sptr;
>- 				/* load first line of entry  */
>-   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
>--    getline(V);
>-+    get_line(V);
>-   if (feof(V->f)) return;
>- 
>-   if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
>-@@ -341,7 +341,7 @@ readPIR(struct ReadSeqVars *V)
>-       SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
>-     }
>-   do {
>--    getline(V);
>-+    get_line(V);
>-     if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
>-       SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
>-     else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
>-@@ -350,7 +350,7 @@ readPIR(struct ReadSeqVars *V)
>- 	  SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
>-       }
>-   } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
>--  getline(V);			/* skip next line, coords */
>-+  get_line(V);			/* skip next line, coords */
>- 
>-   readLoop(0, endPIR, V);
>- 
>-@@ -364,7 +364,7 @@ readPIR(struct ReadSeqVars *V)
>-   /* get next line
>-    */
>-   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
>--    getline(V);
>-+    get_line(V);
>- }
>- 
>- 
>-@@ -382,7 +382,7 @@ readIG(struct ReadSeqVars *V)
>-   char *nm;
>- 				/* position past ';' comments */
>-   do {
>--    getline(V);
>-+    get_line(V);
>-   } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
>- 
>-   if (!feof(V->f))
>-@@ -394,7 +394,7 @@ readIG(struct ReadSeqVars *V)
>-     }
>-   
>-   while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
>--    getline(V);
>-+    get_line(V);
>- }
>- 
>- static int 
>-@@ -416,7 +416,7 @@ readStrider(struct ReadSeqVars *V)
>- 	  if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
>- 	    SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
>- 	}
>--      getline(V);
>-+      get_line(V);
>-     }
>- 
>-   if (! feof(V->f))
>-@@ -425,7 +425,7 @@ readStrider(struct ReadSeqVars *V)
>-   /* load next line
>-    */
>-   while ((!feof(V->f)) && (*V->sbuffer != ';')) 
>--    getline(V);
>-+    get_line(V);
>- }
>- 
>- 
>-@@ -443,7 +443,7 @@ readGenBank(struct ReadSeqVars *V)
>-   int   in_definition;
>- 
>-   while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
>--    getline(V);
>-+    get_line(V);
>- 
>-   if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
>-     {
>-@@ -454,7 +454,7 @@ readGenBank(struct ReadSeqVars *V)
>-   in_definition = FALSE;
>-   while (! feof(V->f))
>-     {
>--      getline(V);
>-+      get_line(V);
>-       if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
>- 	{
>- 	  if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
>-@@ -487,11 +487,11 @@ readGenBank(struct ReadSeqVars *V)
>- 
>- 
>-   while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
>--    getline(V);
>-+    get_line(V);
>- 				/* SRE: V->s now holds "//", so sequential
>- 				   reads are wedged: fixed Tue Jul 13 1993 */
>-   while (!feof(V->f) && strstr(V->sbuffer, "LOCUS  ") != V->sbuffer)
>--    getline(V);
>-+    get_line(V);
>- }
>- 
>- static int
>-@@ -521,12 +521,12 @@ readNBRF(struct ReadSeqVars *V)
>-   if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
>-     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
>- 
>--  getline(V);   /*skip title-junk line*/
>-+  get_line(V);   /*skip title-junk line*/
>- 
>-   readLoop(0, endNBRF, V);
>- 
>-   while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>')))
>--    getline(V);
>-+    get_line(V);
>- }
>- 
>- 
>-@@ -559,7 +559,7 @@ readGCGdata(struct ReadSeqVars *V)
>-   } else Die("bogus GCGdata format? %s", V->sbuffer);
>- 
>- 				/* second line contains free text description */
>--  getline(V);
>-+  get_line(V);
>-   SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
>- 
>-   if (binary) {
>-@@ -579,7 +579,7 @@ readGCGdata(struct ReadSeqVars *V)
>-   else readLoop(0, endGCGdata, V);
>-   
>-   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
>--    getline(V);
>-+    get_line(V);
>- }
>- 
>- static int
>-@@ -625,7 +625,7 @@ readPearson(struct ReadSeqVars *V)
>-     readLoop(0, endPearson, V);
>- 
>-   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
>--    getline(V);
>-+    get_line(V);
>- }
>- 
>- 
>-@@ -652,7 +652,7 @@ readEMBL(struct ReadSeqVars *V)
>- 
>- 				/* make sure we have first line */
>-   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
>--    getline(V);
>-+    get_line(V);
>- 
>-   if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
>-     {
>-@@ -661,7 +661,7 @@ readEMBL(struct ReadSeqVars *V)
>-     }
>- 
>-   do {
>--    getline(V);
>-+    get_line(V);
>-     if (!feof(V->f) && strstr(V->sbuffer, "AC  ") == V->sbuffer)
>-       {
>- 	if ((sptr = strtok(V->sbuffer+5, ";  \t\n")) != NULL)
>-@@ -685,7 +685,7 @@ readEMBL(struct ReadSeqVars *V)
>- 
>- 				/* load next record's ID line */
>-   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
>--    getline(V);
>-+    get_line(V);
>- }
>- 
>- 
>-@@ -701,7 +701,7 @@ readZuker(struct ReadSeqVars *V)
>- {
>-   char *sptr;
>- 
>--  getline(V);  /*s == "seqLen seqid string..."*/
>-+  get_line(V);  /*s == "seqLen seqid string..."*/
>- 
>-   if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
>-     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
>-@@ -712,7 +712,7 @@ readZuker(struct ReadSeqVars *V)
>-   readLoop(0, endZuker, V);
>- 
>-   while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
>--    getline(V);
>-+    get_line(V);
>- }
>- 
>- static void 
>-@@ -734,7 +734,7 @@ readUWGCG(struct ReadSeqVars *V)
>- 
>-   do {
>-     done = feof(V->f);
>--    getline(V);
>-+    get_line(V);
>-     if (! done) addseq(V->sbuffer, V);
>-   } while (!done);
>- }
>-@@ -746,7 +746,7 @@ readSquid(struct ReadSeqVars *V)
>-   char *sptr;
>-   int   dostruc = FALSE;
>- 
>--  while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
>-+  while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
>- 
>-   if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
>-     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
>-@@ -754,7 +754,7 @@ readSquid(struct ReadSeqVars *V)
>-   /*CONSTCOND*/
>-   while (1)
>-     {
>--      getline(V);
>-+      get_line(V);
>-       if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
>- 
>-       if (strncmp(V->sbuffer, "SRC ", 4) == 0)
>-@@ -786,14 +786,14 @@ readSquid(struct ReadSeqVars *V)
>-   while (1)
>-     {
>- 				/* sequence line */
>--      getline(V);
>-+      get_line(V);
>-       if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) 
>- 	break;
>-       addseq(V->sbuffer, V);
>- 				/* structure line */
>-       if (dostruc)
>- 	{
>--	  getline(V);
>-+	  get_line(V);
>- 	  if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
>- 	  addstruc(V->sbuffer, V);
>- 	}
>-@@ -801,7 +801,7 @@ readSquid(struct ReadSeqVars *V)
>- 
>- 
>-   while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
>--    getline(V);
>-+    get_line(V);
>- }
>- 
>- 
>-@@ -848,7 +848,7 @@ SeqfileOpen(char *filename, int format, 
>- 
>-   /* Load the first line.
>-    */
>--  getline(dbfp);
>-+  get_line(dbfp);
>- 
>-   return dbfp;
>- }
>-@@ -862,7 +862,7 @@ void
>- SeqfilePosition(SQFILE *sqfp, long offset)
>- {
>-   fseek(sqfp->f, offset, SEEK_SET);
>--  getline(sqfp);
>-+  get_line(sqfp);
>- }
>- 
>- 
>-@@ -954,7 +954,7 @@ ReadSeq(SQFILE *V, int format, char **re
>- 	do {			/* skip leading comments on GCG file */
>- 	  gotuw = (strstr(V->sbuffer,"..") != NULL);
>- 	  if (gotuw) readUWGCG(V);
>--	  getline(V);
>-+	  get_line(V);
>- 	} while (! feof(V->f));
>- 	break;
>- 
>
>Property changes on: files/patch-sqio.c
>___________________________________________________________________
>Deleted: fbsd:nokeywords
>## -1 +0,0 ##
>-yes
>\ No newline at end of property
>Deleted: svn:eol-style
>## -1 +0,0 ##
>-native
>\ No newline at end of property
>Deleted: svn:mime-type
>## -1 +0,0 ##
>-text/plain
>\ No newline at end of property
>Index: files/patch-tRNAscan-SE.src
>===================================================================
>--- files/patch-tRNAscan-SE.src	(nonexistent)
>+++ files/patch-tRNAscan-SE.src	(working copy)
>@@ -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';
>
>Property changes on: files/patch-tRNAscan-SE.src
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: pkg-descr
>===================================================================
>--- pkg-descr	(revision 471826)
>+++ pkg-descr	(working copy)
>@@ -7,4 +7,4 @@
> 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/
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(nonexistent)
>+++ pkg-plist	(working copy)
>@@ -0,0 +1,136 @@
>+bin/EukHighConfidenceFilter
>+bin/covels-SE
>+bin/coves-SE
>+bin/eufindtRNA
>+bin/fasta2gsi
>+bin/sstofa
>+bin/tRNAscan-SE
>+bin/trnascan-1.4
>+etc/tRNAscan-SE.conf
>+%%DATADIR%%/gcode/gcode.cilnuc
>+%%DATADIR%%/gcode/gcode.echdmito
>+%%DATADIR%%/gcode/gcode.invmito
>+%%DATADIR%%/gcode/gcode.othmito
>+%%DATADIR%%/gcode/gcode.vertmito
>+%%DATADIR%%/gcode/gcode.ystmito
>+%%DATADIR%%/models/Cren-eury-BHB-noncan.cm
>+%%DATADIR%%/models/Dsignal
>+%%DATADIR%%/models/ESELC.cm
>+%%DATADIR%%/models/PSELC.cm
>+%%DATADIR%%/models/TPCsignal
>+%%DATADIR%%/models/TRNA2-arch.cm
>+%%DATADIR%%/models/TRNA2-archns.cm
>+%%DATADIR%%/models/TRNA2-bact.cm
>+%%DATADIR%%/models/TRNA2-bactns.cm
>+%%DATADIR%%/models/TRNA2-euk.cm
>+%%DATADIR%%/models/TRNA2-eukns.cm
>+%%DATADIR%%/models/TRNA2.cm
>+%%DATADIR%%/models/TRNA2ns.cm
>+%%DATADIR%%/models/TRNAinf-1415-ns.cm
>+%%DATADIR%%/models/TRNAinf-1415.cm
>+%%DATADIR%%/models/TRNAinf-arch-3h.cm
>+%%DATADIR%%/models/TRNAinf-arch-5h.cm
>+%%DATADIR%%/models/TRNAinf-arch-SeC.cm
>+%%DATADIR%%/models/TRNAinf-arch-iso
>+%%DATADIR%%/models/TRNAinf-arch-iso.i1f
>+%%DATADIR%%/models/TRNAinf-arch-iso.i1i
>+%%DATADIR%%/models/TRNAinf-arch-iso.i1m
>+%%DATADIR%%/models/TRNAinf-arch-iso.i1p
>+%%DATADIR%%/models/TRNAinf-arch-ns.cm
>+%%DATADIR%%/models/TRNAinf-arch.cm
>+%%DATADIR%%/models/TRNAinf-bact-SeC.cm
>+%%DATADIR%%/models/TRNAinf-bact-iso
>+%%DATADIR%%/models/TRNAinf-bact-iso.i1f
>+%%DATADIR%%/models/TRNAinf-bact-iso.i1i
>+%%DATADIR%%/models/TRNAinf-bact-iso.i1m
>+%%DATADIR%%/models/TRNAinf-bact-iso.i1p
>+%%DATADIR%%/models/TRNAinf-bact-ns.cm
>+%%DATADIR%%/models/TRNAinf-bact.cm
>+%%DATADIR%%/models/TRNAinf-euk-SeC.cm
>+%%DATADIR%%/models/TRNAinf-euk-iso
>+%%DATADIR%%/models/TRNAinf-euk-iso.i1f
>+%%DATADIR%%/models/TRNAinf-euk-iso.i1i
>+%%DATADIR%%/models/TRNAinf-euk-iso.i1m
>+%%DATADIR%%/models/TRNAinf-euk-iso.i1p
>+%%DATADIR%%/models/TRNAinf-euk-ns.cm
>+%%DATADIR%%/models/TRNAinf-euk.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Ala.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Arg.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Asn.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Asp.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Cys.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Gln.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Glu.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Gly.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-His.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Ile.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-LeuTAA.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-LeuTAG.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Lys.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Met.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Phe.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Pro.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-SerGCT.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-SerTGA.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Thr.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Trp.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Tyr.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal-Val.cm
>+%%DATADIR%%/models/TRNAinf-mito-mammal.i1f
>+%%DATADIR%%/models/TRNAinf-mito-mammal.i1i
>+%%DATADIR%%/models/TRNAinf-mito-mammal.i1m
>+%%DATADIR%%/models/TRNAinf-mito-mammal.i1p
>+%%DATADIR%%/models/TRNAinf-mito-vert
>+%%DATADIR%%/models/TRNAinf-mito-vert-Ala.cm
>+%%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.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-Gln.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-Glu.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-Gly.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-His.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-Ile.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-LeuTAA.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-LeuTAG.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-Lys.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-Met.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-Phe.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-Pro.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-SerGCT.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-SerTGA.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-Thr.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-Trp.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-Tyr.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert-Val.cm
>+%%DATADIR%%/models/TRNAinf-mito-vert.i1f
>+%%DATADIR%%/models/TRNAinf-mito-vert.i1i
>+%%DATADIR%%/models/TRNAinf-mito-vert.i1m
>+%%DATADIR%%/models/TRNAinf-mito-vert.i1p
>+%%DATADIR%%/models/TRNAinf-ns.cm
>+%%DATADIR%%/models/TRNAinf.cm
>+%%DATADIR%%/models/Thaum-BHB-noncan.cm
>+%%DATADIR%%/tRNAscanSE/ArrayCMscanResults.pm
>+%%DATADIR%%/tRNAscanSE/ArraytRNA.pm
>+%%DATADIR%%/tRNAscanSE/CM.pm
>+%%DATADIR%%/tRNAscanSE/CMscanResultFile.pm
>+%%DATADIR%%/tRNAscanSE/Configuration.pm
>+%%DATADIR%%/tRNAscanSE/Eufind.pm
>+%%DATADIR%%/tRNAscanSE/FpScanResultFile.pm
>+%%DATADIR%%/tRNAscanSE/GeneticCode.pm
>+%%DATADIR%%/tRNAscanSE/IntResultFile.pm
>+%%DATADIR%%/tRNAscanSE/LogFile.pm
>+%%DATADIR%%/tRNAscanSE/MultiResultFile.pm
>+%%DATADIR%%/tRNAscanSE/Options.pm
>+%%DATADIR%%/tRNAscanSE/ResultFileReader.pm
>+%%DATADIR%%/tRNAscanSE/SS.pm
>+%%DATADIR%%/tRNAscanSE/ScanResult.pm
>+%%DATADIR%%/tRNAscanSE/Sequence.pm
>+%%DATADIR%%/tRNAscanSE/SprinzlAlign.pm
>+%%DATADIR%%/tRNAscanSE/SprinzlAlignResults.pm
>+%%DATADIR%%/tRNAscanSE/SprinzlPos.pm
>+%%DATADIR%%/tRNAscanSE/Stats.pm
>+%%DATADIR%%/tRNAscanSE/Tscan.pm
>+%%DATADIR%%/tRNAscanSE/Utils.pm
>+%%DATADIR%%/tRNAscanSE/tRNA.pm
>
>Property changes on: pkg-plist
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property

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Attachments on bug 228758: 194013 | 194016 | 194046