8 files changed, 121 insertions, 345 deletions

diff --git a/biology/tRNAscan-SE/Makefile b/biology/tRNAscan-SE/Makefile
index 5795c2ec4f10..0113dd4692fe 100644
--- a/biology/tRNAscan-SE/Makefile
+++ b/biology/tRNAscan-SE/Makefile
@@ -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/
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Improved tool for transfer RNA detection
-
-BROKEN=		No public distfiles
-DEPRECATED=	Broken for more than 6 months
-EXPIRATION_DATE=	2018-06-06
-
-USES=		perl5 tar:Z
-MAKE_ARGS=	BINDIR="${PREFIX}/bin" \
-		LIBDIR="${DATADIR}" \
-		CC="${CC}" \
-		CFLAGS="${CFLAGS}"
-
-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
-
-OPTIONS_DEFINE=	DOCS
-
-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}
+MASTER_SITES=	http://lowelab.ucsc.edu/software/
+DISTFILES=	${DISTNAME:tl}${EXTRACT_SUFX}
+
+MAINTAINER=	mzaki@niid.go.jp
+COMMENT=	Searching for tRNA genes in genomic sequence
+
+LICENSE=	GPLv3+
+LICENSE_FILE=	${WRKSRC}/COPYING
+
+RUN_DEPENDS=	cmsearch:biology/infernal
+
+WRKSRC=		${WRKDIR}/${DISTNAME:S,.0$,,}
+
+GNU_CONFIGURE=	yes
+
+USES=		perl5 autoreconf
 
 .include <bsd.port.mk>
diff --git a/biology/tRNAscan-SE/distinfo b/biology/tRNAscan-SE/distinfo
index 82bd9aad6296..fce995d4414e 100644
--- a/biology/tRNAscan-SE/distinfo
+++ b/biology/tRNAscan-SE/distinfo
@@ -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
diff --git a/biology/tRNAscan-SE/files/patch-Makefile b/biology/tRNAscan-SE/files/patch-Makefile
deleted file mode 100644
index b9e2c9aa2f07..000000000000
--- a/biology/tRNAscan-SE/files/patch-Makefile
+++ /dev/null
@@ -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)
diff --git a/biology/tRNAscan-SE/files/patch-Makefile.am b/biology/tRNAscan-SE/files/patch-Makefile.am
new file mode 100644
index 000000000000..7a28de19c450
--- /dev/null
+++ b/biology/tRNAscan-SE/files/patch-Makefile.am
@@ -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/*
diff --git a/biology/tRNAscan-SE/files/patch-configure.ac b/biology/tRNAscan-SE/files/patch-configure.ac
new file mode 100644
index 000000000000..af9604d55a64
--- /dev/null
+++ b/biology/tRNAscan-SE/files/patch-configure.ac
@@ -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])
diff --git a/biology/tRNAscan-SE/files/patch-sqio.c b/biology/tRNAscan-SE/files/patch-sqio.c
deleted file mode 100644
index 62591b3555ba..000000000000
--- a/biology/tRNAscan-SE/files/patch-sqio.c
+++ /dev/null
@@ -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;
- 
diff --git a/biology/tRNAscan-SE/files/patch-tRNAscan-SE.src b/biology/tRNAscan-SE/files/patch-tRNAscan-SE.src
new file mode 100644
index 000000000000..8bb7d492e25f
--- /dev/null
+++ b/biology/tRNAscan-SE/files/patch-tRNAscan-SE.src
@@ -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';
diff --git a/biology/tRNAscan-SE/pkg-descr b/biology/tRNAscan-SE/pkg-descr
index 288f622a4c1c..4e6dafa3c065 100644
--- a/biology/tRNAscan-SE/pkg-descr
+++ b/biology/tRNAscan-SE/pkg-descr
@@ -7,4 +7,4 @@ the flow of information between them, performing a limited amount of
 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/