Attachment #194046 for bug #228758




# $FreeBSD$

PORTNAME=	tRNAscan-SE
PORTVERSION=	2.0.0
PORTREVISION=	1
CATEGORIES=	biology
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
EXPIRATION_DATE=	2018-06-06

RUN_DEPENDS=	cmsearch:biology/infernal
MAKE_ARGS=	BINDIR="${PREFIX}/bin" \
		LIBDIR="${DATADIR}" \
		CC="${CC}" \
		CFLAGS="${CFLAGS}"

WRKSRC=		${WRKDIR}/${DISTNAME:S,.0$,,}
		man/man1/tRNAscan-SE.1.gz
PORTDATA=	*
PORTDOCS=	Manual.ps

GNU_CONFIGURE=	yes

USES=		perl5 autoreconf
	@${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}

.include <bsd.port.mk>

Lines 1-2 Link Here

(-)distinfo (-2 / +3 lines)
1	SHA256 (tRNAscan-SE-1.23.tar.Z) = 843caf3e258a6293300513ddca7eb7dbbd2225e5baae1e5a7bcafd509f6dd550	1	TIMESTAMP = 1528270436
2	SIZE (tRNAscan-SE-1.23.tar.Z) = 846349	2	SHA256 (trnascan-se-2.0.0.tar.gz) = 0dde1c07142e4bf77b21d53ddf3eeb1ef8c52248005a42323d13f8d7c798100c
		3	SIZE (trnascan-se-2.0.0.tar.gz) = 4372755

Lines 1-11 Link Here

(-)files/patch-Makefile (-11 lines)
1	--- Makefile.orig 2013-03-17 11:38:57.213776000 +0000
2	+++ Makefile
3	@@ -13,7 +13,7 @@ RFLAGS = -DRELEASE=$(COV_RELEASE) -D
4	## greatly speeding scans of unfinished sequence
5
6	## where Perl v.5 (or greater) is installed
7	-PERLDIR = /usr/bin
8	+PERLDIR = $(PREFIX)/bin
9
10	## what you call the Perl v.5 executable on your system
11	## (this could be 'perl5' or otherwise on some systems)




--- 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/*




--- 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])




--- 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;
 




--- 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';

Lines 7-10 Link Here

(-)pkg-descr (-1 / +1 lines)
7	post-processing, and outputting the results in one of several	7	post-processing, and outputting the results in one of several
8	formats.	8	formats.
9		9
10	WWW: http://selab.janelia.org/software.html	10	WWW: http://lowelab.ucsc.edu/tRNAscan-SE/




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

Return to bug 228758

Lines 2-47 Link Here

(-)Makefile (-34 / +11 lines)
2	# $FreeBSD$	2	# $FreeBSD$
3		3
4	PORTNAME= tRNAscan-SE	4	PORTNAME= tRNAscan-SE
5	PORTVERSION= 1.23	5	PORTVERSION= 2.0.0
6	PORTREVISION= 1
7	CATEGORIES= biology	6	CATEGORIES= biology
8	MASTER_SITES= ftp://selab.janelia.org/pub/software/tRNAscan-SE/	7	MASTER_SITES= http://lowelab.ucsc.edu/software/
		8	DISTFILES= ${DISTNAME:tl}${EXTRACT_SUFX}
9		9
10	MAINTAINER= ports@FreeBSD.org	10	MAINTAINER= mzaki@niid.go.jp
11	COMMENT= Improved tool for transfer RNA detection	11	COMMENT= Searching for tRNA genes in genomic sequence
12		12
13	BROKEN= No public distfiles	13	LICENSE= GPLv3+
14	DEPRECATED= Broken for more than 6 months	14	LICENSE_FILE= ${WRKSRC}/COPYING
15	EXPIRATION_DATE= 2018-06-06
16		15
17	USES= perl5 tar:Z	16	RUN_DEPENDS= cmsearch:biology/infernal
18	MAKE_ARGS= BINDIR="${PREFIX}/bin" \
19	LIBDIR="${DATADIR}" \
20	CC="${CC}" \
21	CFLAGS="${CFLAGS}"
22		17
23	PLIST_FILES+= bin/covels-SE bin/coves-SE bin/eufindtRNA bin/tRNAscan-SE bin/trnascan-1.4 \	18	WRKSRC= ${WRKDIR}/${DISTNAME:S,.0$,,}
24	man/man1/tRNAscan-SE.1.gz
25	PORTDATA= *
26	PORTDOCS= Manual.ps
27		19
28	OPTIONS_DEFINE= DOCS	20	GNU_CONFIGURE= yes
29		21
30	post-patch:	22	USES= perl5 autoreconf
31	@${REINPLACE_CMD} -e 's\|tRNAscanSE setpaths\|tRNAscanSE\|g ; \
32	s\|if tRNAscan-SE\|if ./tRNAscan-SE\|g' ${WRKSRC}/Makefile
33		23
34	do-install:
35	.for f in covels-SE coves-SE eufindtRNA trnascan-1.4
36	${INSTALL_PROGRAM} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin
37	.endfor
38	${INSTALL_SCRIPT} ${WRKSRC}/tRNAscan-SE ${STAGEDIR}${PREFIX}/bin
39	${INSTALL_MAN} ${WRKSRC}/tRNAscan-SE.man ${STAGEDIR}${MANPREFIX}/man/man1/tRNAscan-SE.1
40	@${MKDIR} ${STAGEDIR}${DATADIR}
41	.for f in TPCsignal Dsignal .cm gcode.
42	${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DATADIR}
43	.endfor
44	@${MKDIR} ${STAGEDIR}${DOCSDIR}
45	${INSTALL_DATA} ${WRKSRC}/Manual.ps ${STAGEDIR}${DOCSDIR}
46
47	.include <bsd.port.mk>	24	.include <bsd.port.mk>

Line 0 Link Here

(-)files/patch-Makefile.am (+62 lines)
	1	--- Makefile.am.orig 2017-12-03 07:00:58 UTC
	2	+++ Makefile.am
	3	@@ -8,8 +8,8 @@
	4	AUTOMAKE_OPTIONS = foreign subdir-objects
	5
	6	# set flags
	7	-AM_CFLAGS = -O
	8	-LDADD = -lm
	9	+#AM_CFLAGS = -O
	10	+#LDADD = -lm
	11
	12	# macros for program dependencies
	13	EUFIND = src/eufind_const.h src/eufind_main.c src/pavesi.c
	14	@@ -23,20 +23,21 @@ COVESRC = src/align.c src/dbviterbi.c sr
	15	bin_PROGRAMS = bin/eufindtRNA bin/trnascan-1.4 bin/covels-SE bin/coves-SE
	16	bin_eufindtRNA_SOURCES = $(SQUIDHDRS) $(SQUIDSRC) $(EUFIND)
	17	bin_trnascan_1_4_SOURCES = src/trnascan.c
	18	-bin_trnascan_1_4_CFLAGS = -DTSCANDIR=\"$(libdir)\/tRNAscan-SE\/models\" $(AM_CFLAGS)
	19	+bin_trnascan_1_4_CFLAGS = -DTSCANDIR=\"$(datadir)\/tRNAscan-SE\/models\" $(AM_CFLAGS)
	20	bin_covels_SE_SOURCES = $(COVESRC) src/scan_main.c
	21	bin_coves_SE_SOURCES = $(COVESRC) src/score_main.c
	22
	23	# process scripts
	24	# treat tRNAscan-SE.conf as a script since it's just easier
	25	-dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter tRNAscan-SE tRNAscan-SE.conf
	26	+dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter tRNAscan-SE
	27	+sysconf_DATA = tRNAscan-SE.conf
	28	# for a few files, need to substitute perl path, bin directory, and lib directory
	29	# first, define a function for it
	30	-do_subst = sed -e 's,\@bindir\@,$(bindir),g' -e 's,\@libdir\@,$(libdir),g' -e 's,[@]PERL[@],$(PERL),g' -e 's,\@INFERNAL\@,$(INFERNAL),g'
	31	+do_subst = sed -e 's,\@bindir\@,$(bindir),g' -e 's,\@libdir\@,$(datadir),g' -e 's,\@sysconfdir\@,$(sysconfdir),g' -e 's,[@]PERL[@],$(PERL),g' -e 's,\@INFERNAL\@,$(INFERNAL),g'
	32
	33	# extra steps for cleaning/distribution
	34	CLEANFILES = $(dist_bin_SCRIPTS) $(srcdir)/lib/*
	35	-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
	38
	39	# then create build rules
	40	@@ -61,16 +62,9 @@ bin/EukHighConfidenceFilter: EukHighConf
	41	$(do_subst) < $(srcdir)/EukHighConfidenceFilter.in > bin/EukHighConfidenceFilter
	42	chmod +x bin/EukHighConfidenceFilter
	43
	44	-# 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.
	45	-install-data-hook:
	46	- chmod u+w $(exec_prefix)
	47	- test -d $(libdir) \|\| mkdir $(libdir)
	48	- chmod u+w $(libdir)
	49	- test -d $(libdir)/tRNAscan-SE \|\| mkdir $(libdir)/tRNAscan-SE
	50	- cp -rf $(srcdir)/lib/* $(libdir)/tRNAscan-SE
	51	-
	52	-# remove lib/ files during uninstallation. A bit of a hack, since lib files are write-protected by default. Files
	53	-uninstall-hook:
	54	- chmod -R u+w $(libdir)/tRNAscan-SE
	55	- rm -rf $(libdir)/tRNAscan-SE
	56	-
	57	+gcodedir = $(pkgdatadir)/gcode
	58	+modelsdir = $(pkgdatadir)/models
	59	+modulesdir = $(pkgdatadir)/tRNAscanSE
	60	+dist_gcode_DATA = lib/gcode/*
	61	+dist_models_DATA = lib/models/*
	62	+dist_modules_DATA = lib/tRNAscanSE/*

Line 0 Link Here

(-)files/patch-configure.ac (+21 lines)
	1	--- configure.ac.orig 2017-04-27 20:18:19 UTC
	2	+++ configure.ac
	3	@@ -4,7 +4,7 @@
	4	## Settings for generating a configure file
	5
	6	AC_PREREQ([2.69])
	7	-AC_INIT([tRNAscan-SE],[2.0.0],[pchan@soe.ucsc.edu])
	8	+AC_INIT([tRNAscan-SE],[2.0.0],[pchan@soe.ucsc.edu],[tRNAscan-SE])
	9	AC_CONFIG_HEADERS([config.h])
	10
	11	# Checks for programs.
	12	@@ -33,7 +33,8 @@ AC_TYPE_SIZE_T
	13	# Checks for library functions.
	14	AC_FUNC_MALLOC
	15	AC_FUNC_REALLOC
	16	-AC_CHECK_FUNCS([bzero memset re_comp regcomp sqrt strcasecmp strchr strstr])
	17	+AC_CHECK_FUNCS([bzero memset re_comp regcomp strcasecmp strchr strstr])
	18	+AC_SEARCH_LIBS([sqrt],[m])
	19
	20	# use automake
	21	AM_INIT_AUTOMAKE([foreign])

Lines 1-291 Link Here

(-)files/patch-sqio.c (-291 lines)
1	--- sqio.c.orig 2002-04-12 20:12:04 UTC
2	+++ sqio.c
3	@@ -235,7 +235,7 @@ readline(FILE f, char s)
4	}
5
6	static void
7	-getline(struct ReadSeqVars *V)
8	+get_line(struct ReadSeqVars *V)
9	{
10	readline(V->f, V->sbuffer);
11	}
12	@@ -306,7 +306,7 @@ readLoop(int addfirst, int (*endTest)(ch
13	V->seqlen = 0;
14	if (addfirst) addseq(V->sbuffer, V);
15	do {
16	- getline(V);
17	+ get_line(V);
18	done = feof(V->f);
19	done \|= (*endTest)(V->sbuffer, &addend);
20	if (addend \|\| !done)
21	@@ -332,7 +332,7 @@ readPIR(struct ReadSeqVars *V)
22	char *sptr;
23	/* load first line of entry */
24	while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
25	- getline(V);
26	+ get_line(V);
27	if (feof(V->f)) return;
28
29	if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
30	@@ -341,7 +341,7 @@ readPIR(struct ReadSeqVars *V)
31	SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
32	}
33	do {
34	- getline(V);
35	+ get_line(V);
36	if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
37	SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
38	else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
39	@@ -350,7 +350,7 @@ readPIR(struct ReadSeqVars *V)
40	SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
41	}
42	} while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
43	- getline(V); /* skip next line, coords */
44	+ get_line(V); /* skip next line, coords */
45
46	readLoop(0, endPIR, V);
47
48	@@ -364,7 +364,7 @@ readPIR(struct ReadSeqVars *V)
49	/* get next line
50	*/
51	while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
52	- getline(V);
53	+ get_line(V);
54	}
55
56
57	@@ -382,7 +382,7 @@ readIG(struct ReadSeqVars *V)
58	char *nm;
59	/* position past ';' comments */
60	do {
61	- getline(V);
62	+ get_line(V);
63	} while (! (feof(V->f) \|\| ((V->sbuffer != 0) && (V->sbuffer != ';')) ));
64
65	if (!feof(V->f))
66	@@ -394,7 +394,7 @@ readIG(struct ReadSeqVars *V)
67	}
68
69	while (!(feof(V->f) \|\| ((V->sbuffer != '\0') && (V->sbuffer == ';'))))
70	- getline(V);
71	+ get_line(V);
72	}
73
74	static int
75	@@ -416,7 +416,7 @@ readStrider(struct ReadSeqVars *V)
76	if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
77	SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
78	}
79	- getline(V);
80	+ get_line(V);
81	}
82
83	if (! feof(V->f))
84	@@ -425,7 +425,7 @@ readStrider(struct ReadSeqVars *V)
85	/* load next line
86	*/
87	while ((!feof(V->f)) && (*V->sbuffer != ';'))
88	- getline(V);
89	+ get_line(V);
90	}
91
92
93	@@ -443,7 +443,7 @@ readGenBank(struct ReadSeqVars *V)
94	int in_definition;
95
96	while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
97	- getline(V);
98	+ get_line(V);
99
100	if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
101	{
102	@@ -454,7 +454,7 @@ readGenBank(struct ReadSeqVars *V)
103	in_definition = FALSE;
104	while (! feof(V->f))
105	{
106	- getline(V);
107	+ get_line(V);
108	if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
109	{
110	if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
111	@@ -487,11 +487,11 @@ readGenBank(struct ReadSeqVars *V)
112
113
114	while (!(feof(V->f) \|\| ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
115	- getline(V);
116	+ get_line(V);
117	/* SRE: V->s now holds "//", so sequential
118	reads are wedged: fixed Tue Jul 13 1993 */
119	while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
120	- getline(V);
121	+ get_line(V);
122	}
123
124	static int
125	@@ -521,12 +521,12 @@ readNBRF(struct ReadSeqVars *V)
126	if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
127	SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
128
129	- getline(V); /skip title-junk line/
130	+ get_line(V); /skip title-junk line/
131
132	readLoop(0, endNBRF, V);
133
134	while (!(feof(V->f) \|\| (V->sbuffer != 0 && V->sbuffer == '>')))
135	- getline(V);
136	+ get_line(V);
137	}
138
139
140	@@ -559,7 +559,7 @@ readGCGdata(struct ReadSeqVars *V)
141	} else Die("bogus GCGdata format? %s", V->sbuffer);
142
143	/* second line contains free text description */
144	- getline(V);
145	+ get_line(V);
146	SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
147
148	if (binary) {
149	@@ -579,7 +579,7 @@ readGCGdata(struct ReadSeqVars *V)
150	else readLoop(0, endGCGdata, V);
151
152	while (!(feof(V->f) \|\| ((V->sbuffer != 0) && (V->sbuffer == '>'))))
153	- getline(V);
154	+ get_line(V);
155	}
156
157	static int
158	@@ -625,7 +625,7 @@ readPearson(struct ReadSeqVars *V)
159	readLoop(0, endPearson, V);
160
161	while (!(feof(V->f) \|\| ((V->sbuffer != 0) && (V->sbuffer == '>'))))
162	- getline(V);
163	+ get_line(V);
164	}
165
166
167	@@ -652,7 +652,7 @@ readEMBL(struct ReadSeqVars *V)
168
169	/* make sure we have first line */
170	while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
171	- getline(V);
172	+ get_line(V);
173
174	if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
175	{
176	@@ -661,7 +661,7 @@ readEMBL(struct ReadSeqVars *V)
177	}
178
179	do {
180	- getline(V);
181	+ get_line(V);
182	if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
183	{
184	if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
185	@@ -685,7 +685,7 @@ readEMBL(struct ReadSeqVars *V)
186
187	/* load next record's ID line */
188	while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
189	- getline(V);
190	+ get_line(V);
191	}
192
193
194	@@ -701,7 +701,7 @@ readZuker(struct ReadSeqVars *V)
195	{
196	char *sptr;
197
198	- getline(V); /s == "seqLen seqid string..."/
199	+ get_line(V); /s == "seqLen seqid string..."/
200
201	if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
202	SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
203	@@ -712,7 +712,7 @@ readZuker(struct ReadSeqVars *V)
204	readLoop(0, endZuker, V);
205
206	while (!(feof(V->f) \| ((V->sbuffer != '\0') & (V->sbuffer == '('))))
207	- getline(V);
208	+ get_line(V);
209	}
210
211	static void
212	@@ -734,7 +734,7 @@ readUWGCG(struct ReadSeqVars *V)
213
214	do {
215	done = feof(V->f);
216	- getline(V);
217	+ get_line(V);
218	if (! done) addseq(V->sbuffer, V);
219	} while (!done);
220	}
221	@@ -746,7 +746,7 @@ readSquid(struct ReadSeqVars *V)
222	char *sptr;
223	int dostruc = FALSE;
224
225	- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
226	+ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
227
228	if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
229	SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
230	@@ -754,7 +754,7 @@ readSquid(struct ReadSeqVars *V)
231	/CONSTCOND/
232	while (1)
233	{
234	- getline(V);
235	+ get_line(V);
236	if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
237
238	if (strncmp(V->sbuffer, "SRC ", 4) == 0)
239	@@ -786,14 +786,14 @@ readSquid(struct ReadSeqVars *V)
240	while (1)
241	{
242	/* sequence line */
243	- getline(V);
244	+ get_line(V);
245	if (feof(V->f) \|\| strncmp(V->sbuffer, "++", 2) == 0)
246	break;
247	addseq(V->sbuffer, V);
248	/* structure line */
249	if (dostruc)
250	{
251	- getline(V);
252	+ get_line(V);
253	if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
254	addstruc(V->sbuffer, V);
255	}
256	@@ -801,7 +801,7 @@ readSquid(struct ReadSeqVars *V)
257
258
259	while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
260	- getline(V);
261	+ get_line(V);
262	}
263
264
265	@@ -848,7 +848,7 @@ SeqfileOpen(char *filename, int format,
266
267	/* Load the first line.
268	*/
269	- getline(dbfp);
270	+ get_line(dbfp);
271
272	return dbfp;
273	}
274	@@ -862,7 +862,7 @@ void
275	SeqfilePosition(SQFILE *sqfp, long offset)
276	{
277	fseek(sqfp->f, offset, SEEK_SET);
278	- getline(sqfp);
279	+ get_line(sqfp);
280	}
281
282
283	@@ -954,7 +954,7 @@ ReadSeq(SQFILE V, int format, char *re
284	do { /* skip leading comments on GCG file */
285	gotuw = (strstr(V->sbuffer,"..") != NULL);
286	if (gotuw) readUWGCG(V);
287	- getline(V);
288	+ get_line(V);
289	} while (! feof(V->f));
290	break;
291

Line 0 Link Here

(-)files/patch-tRNAscan-SE.src (+17 lines)
	1	--- tRNAscan-SE.src.orig 2017-12-03 01:59:25 UTC
	2	+++ tRNAscan-SE.src
	3	@@ -1,4 +1,4 @@
	4	-#! /usr/bin/perl
	5	+#! @PERL@
	6	#
	7	# --------------------------------------------------------------------
	8	# tRNAscan-SE: a program for improved detection of transfer RNA
	9	@@ -44,7 +44,7 @@ our $release_date = "December 2017";
	10	our $program_id = "tRNAscan-SE-".$version;
	11
	12	# modified by 'make'
	13	-our $default_conf = "@bindir@/tRNAscan-SE.conf";
	14	+our $default_conf = "@sysconfdir@/tRNAscan-SE.conf";
	15
	16	# Signal handling
	17	$SIG{'TERM'} = 'error_handler';

Line 0 Link Here

(-)pkg-plist (+136 lines)
		1	bin/EukHighConfidenceFilter
		2	bin/covels-SE
		3	bin/coves-SE
		4	bin/eufindtRNA
		5	bin/fasta2gsi
		6	bin/sstofa
		7	bin/tRNAscan-SE
		8	bin/trnascan-1.4
		9	etc/tRNAscan-SE.conf
		10	%%DATADIR%%/gcode/gcode.cilnuc
		11	%%DATADIR%%/gcode/gcode.echdmito
		12	%%DATADIR%%/gcode/gcode.invmito
		13	%%DATADIR%%/gcode/gcode.othmito
		14	%%DATADIR%%/gcode/gcode.vertmito
		15	%%DATADIR%%/gcode/gcode.ystmito
		16	%%DATADIR%%/models/Cren-eury-BHB-noncan.cm
		17	%%DATADIR%%/models/Dsignal
		18	%%DATADIR%%/models/ESELC.cm
		19	%%DATADIR%%/models/PSELC.cm
		20	%%DATADIR%%/models/TPCsignal
		21	%%DATADIR%%/models/TRNA2-arch.cm
		22	%%DATADIR%%/models/TRNA2-archns.cm
		23	%%DATADIR%%/models/TRNA2-bact.cm
		24	%%DATADIR%%/models/TRNA2-bactns.cm
		25	%%DATADIR%%/models/TRNA2-euk.cm
		26	%%DATADIR%%/models/TRNA2-eukns.cm
		27	%%DATADIR%%/models/TRNA2.cm
		28	%%DATADIR%%/models/TRNA2ns.cm
		29	%%DATADIR%%/models/TRNAinf-1415-ns.cm
		30	%%DATADIR%%/models/TRNAinf-1415.cm
		31	%%DATADIR%%/models/TRNAinf-arch-3h.cm
		32	%%DATADIR%%/models/TRNAinf-arch-5h.cm
		33	%%DATADIR%%/models/TRNAinf-arch-SeC.cm
		34	%%DATADIR%%/models/TRNAinf-arch-iso
		35	%%DATADIR%%/models/TRNAinf-arch-iso.i1f
		36	%%DATADIR%%/models/TRNAinf-arch-iso.i1i
		37	%%DATADIR%%/models/TRNAinf-arch-iso.i1m
		38	%%DATADIR%%/models/TRNAinf-arch-iso.i1p
		39	%%DATADIR%%/models/TRNAinf-arch-ns.cm
		40	%%DATADIR%%/models/TRNAinf-arch.cm
		41	%%DATADIR%%/models/TRNAinf-bact-SeC.cm
		42	%%DATADIR%%/models/TRNAinf-bact-iso
		43	%%DATADIR%%/models/TRNAinf-bact-iso.i1f
		44	%%DATADIR%%/models/TRNAinf-bact-iso.i1i
		45	%%DATADIR%%/models/TRNAinf-bact-iso.i1m
		46	%%DATADIR%%/models/TRNAinf-bact-iso.i1p
		47	%%DATADIR%%/models/TRNAinf-bact-ns.cm
		48	%%DATADIR%%/models/TRNAinf-bact.cm
		49	%%DATADIR%%/models/TRNAinf-euk-SeC.cm
		50	%%DATADIR%%/models/TRNAinf-euk-iso
		51	%%DATADIR%%/models/TRNAinf-euk-iso.i1f
		52	%%DATADIR%%/models/TRNAinf-euk-iso.i1i
		53	%%DATADIR%%/models/TRNAinf-euk-iso.i1m
		54	%%DATADIR%%/models/TRNAinf-euk-iso.i1p
		55	%%DATADIR%%/models/TRNAinf-euk-ns.cm
		56	%%DATADIR%%/models/TRNAinf-euk.cm
		57	%%DATADIR%%/models/TRNAinf-mito-mammal
		58	%%DATADIR%%/models/TRNAinf-mito-mammal-Ala.cm
		59	%%DATADIR%%/models/TRNAinf-mito-mammal-Arg.cm
		60	%%DATADIR%%/models/TRNAinf-mito-mammal-Asn.cm
		61	%%DATADIR%%/models/TRNAinf-mito-mammal-Asp.cm
		62	%%DATADIR%%/models/TRNAinf-mito-mammal-Cys.cm
		63	%%DATADIR%%/models/TRNAinf-mito-mammal-Gln.cm
		64	%%DATADIR%%/models/TRNAinf-mito-mammal-Glu.cm
65	%%DATADIR%%/models/TRNAinf-mito-mammal-Gly.cm
66	%%DATADIR%%/models/TRNAinf-mito-mammal-His.cm
67	%%DATADIR%%/models/TRNAinf-mito-mammal-Ile.cm
68	%%DATADIR%%/models/TRNAinf-mito-mammal-LeuTAA.cm
69	%%DATADIR%%/models/TRNAinf-mito-mammal-LeuTAG.cm
70	%%DATADIR%%/models/TRNAinf-mito-mammal-Lys.cm
71	%%DATADIR%%/models/TRNAinf-mito-mammal-Met.cm
72	%%DATADIR%%/models/TRNAinf-mito-mammal-Phe.cm
73	%%DATADIR%%/models/TRNAinf-mito-mammal-Pro.cm
74	%%DATADIR%%/models/TRNAinf-mito-mammal-SerGCT.cm
75	%%DATADIR%%/models/TRNAinf-mito-mammal-SerTGA.cm
76	%%DATADIR%%/models/TRNAinf-mito-mammal-Thr.cm
77	%%DATADIR%%/models/TRNAinf-mito-mammal-Trp.cm
78	%%DATADIR%%/models/TRNAinf-mito-mammal-Tyr.cm
79	%%DATADIR%%/models/TRNAinf-mito-mammal-Val.cm
80	%%DATADIR%%/models/TRNAinf-mito-mammal.i1f
81	%%DATADIR%%/models/TRNAinf-mito-mammal.i1i
82	%%DATADIR%%/models/TRNAinf-mito-mammal.i1m
83	%%DATADIR%%/models/TRNAinf-mito-mammal.i1p
84	%%DATADIR%%/models/TRNAinf-mito-vert
85	%%DATADIR%%/models/TRNAinf-mito-vert-Ala.cm
86	%%DATADIR%%/models/TRNAinf-mito-vert-Arg.cm
87	%%DATADIR%%/models/TRNAinf-mito-vert-Asn.cm
88	%%DATADIR%%/models/TRNAinf-mito-vert-Asp.cm
89	%%DATADIR%%/models/TRNAinf-mito-vert-Cys.cm
90	%%DATADIR%%/models/TRNAinf-mito-vert-Gln.cm
91	%%DATADIR%%/models/TRNAinf-mito-vert-Glu.cm
92	%%DATADIR%%/models/TRNAinf-mito-vert-Gly.cm
93	%%DATADIR%%/models/TRNAinf-mito-vert-His.cm
94	%%DATADIR%%/models/TRNAinf-mito-vert-Ile.cm
95	%%DATADIR%%/models/TRNAinf-mito-vert-LeuTAA.cm
96	%%DATADIR%%/models/TRNAinf-mito-vert-LeuTAG.cm
97	%%DATADIR%%/models/TRNAinf-mito-vert-Lys.cm
98	%%DATADIR%%/models/TRNAinf-mito-vert-Met.cm
99	%%DATADIR%%/models/TRNAinf-mito-vert-Phe.cm
100	%%DATADIR%%/models/TRNAinf-mito-vert-Pro.cm
101	%%DATADIR%%/models/TRNAinf-mito-vert-SerGCT.cm
102	%%DATADIR%%/models/TRNAinf-mito-vert-SerTGA.cm
103	%%DATADIR%%/models/TRNAinf-mito-vert-Thr.cm
104	%%DATADIR%%/models/TRNAinf-mito-vert-Trp.cm
105	%%DATADIR%%/models/TRNAinf-mito-vert-Tyr.cm
106	%%DATADIR%%/models/TRNAinf-mito-vert-Val.cm
107	%%DATADIR%%/models/TRNAinf-mito-vert.i1f
108	%%DATADIR%%/models/TRNAinf-mito-vert.i1i
109	%%DATADIR%%/models/TRNAinf-mito-vert.i1m
110	%%DATADIR%%/models/TRNAinf-mito-vert.i1p
111	%%DATADIR%%/models/TRNAinf-ns.cm
112	%%DATADIR%%/models/TRNAinf.cm
113	%%DATADIR%%/models/Thaum-BHB-noncan.cm
114	%%DATADIR%%/tRNAscanSE/ArrayCMscanResults.pm
115	%%DATADIR%%/tRNAscanSE/ArraytRNA.pm
116	%%DATADIR%%/tRNAscanSE/CM.pm
117	%%DATADIR%%/tRNAscanSE/CMscanResultFile.pm
118	%%DATADIR%%/tRNAscanSE/Configuration.pm
119	%%DATADIR%%/tRNAscanSE/Eufind.pm
120	%%DATADIR%%/tRNAscanSE/FpScanResultFile.pm
121	%%DATADIR%%/tRNAscanSE/GeneticCode.pm
122	%%DATADIR%%/tRNAscanSE/IntResultFile.pm
123	%%DATADIR%%/tRNAscanSE/LogFile.pm
124	%%DATADIR%%/tRNAscanSE/MultiResultFile.pm
125	%%DATADIR%%/tRNAscanSE/Options.pm
126	%%DATADIR%%/tRNAscanSE/ResultFileReader.pm
127	%%DATADIR%%/tRNAscanSE/SS.pm
128	%%DATADIR%%/tRNAscanSE/ScanResult.pm
129	%%DATADIR%%/tRNAscanSE/Sequence.pm
130	%%DATADIR%%/tRNAscanSE/SprinzlAlign.pm
131	%%DATADIR%%/tRNAscanSE/SprinzlAlignResults.pm
132	%%DATADIR%%/tRNAscanSE/SprinzlPos.pm
133	%%DATADIR%%/tRNAscanSE/Stats.pm
134	%%DATADIR%%/tRNAscanSE/Tscan.pm
135	%%DATADIR%%/tRNAscanSE/Utils.pm
136	%%DATADIR%%/tRNAscanSE/tRNA.pm