diff options
Diffstat (limited to 'sci-biology/trnascan-se')
7 files changed, 280 insertions, 81 deletions
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch new file mode 100644 index 000000000000..33889c90cf69 --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch @@ -0,0 +1,62 @@ +https://bugs.gentoo.org/874477 +--- a/eufind_main.c ++++ b/eufind_main.c +@@ -23,4 +23,5 @@ + #include <stdlib.h> + #include <string.h> ++#include <unistd.h> + #include "squid.h" + #include "sqfuncs.h" +@@ -47,4 +48,14 @@ + -i <integer> : start nucleotide numbering at <integer> (def=1)\n\n"; + ++int GetBbox(float*, int*, char*, int, int, int); ++int GetBestABox(TRNA_TYPE*, char*, char*, int, int, int, int, int); ++int GetBestTrxTerm(TRNA_TYPE*, char*, int, float); ++int GetSecABox(TRNA_TYPE*, char*); ++void Get_tRNA_stats(TRNA_TYPE*, char*, int, int); ++int Init_tRNA(TRNA_TYPE*); ++int IntEncodeSeq(char*, char*, int); ++void Save_tRNA(TRNA_TYPE*, SQINFO*, char*, int, int, long int); ++int tRNAOverlap(TRNA_TYPE*, TRNA_TYPE*, int); ++ + int + main (int argc, char **argv) +--- a/scan_main.c ++++ b/scan_main.c +@@ -8,4 +8,5 @@ + #include <stdlib.h> + #include <string.h> ++#include <unistd.h> + #include <time.h> + #include <math.h> +--- a/score_main.c ++++ b/score_main.c +@@ -10,4 +10,5 @@ + #include <stdlib.h> + #include <string.h> ++#include <unistd.h> + #include <time.h> + #include <math.h> +--- a/trnascan.c ++++ b/trnascan.c +@@ -69,4 +69,5 @@ + #include <stdio.h> + #include <stdlib.h> ++#include <unistd.h> + #include <ctype.h> + +@@ -333,5 +334,5 @@ + ); + +-main(int argc, char **argv) ++int main(int argc, char **argv) + { + /* pointers to the different files fpi=input file, fpo=output file, +@@ -1419,5 +1420,5 @@ + /* Calls to this function eliminated for efficiency T. Lowe 11/95 */ + +-myindex (char *s, char *t) ++int myindex (char *s, char *t) + { + int i, j, k; diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch deleted file mode 100644 index f28b1e8f6bb0..000000000000 --- a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch +++ /dev/null @@ -1,26 +0,0 @@ -diff --git a/Makefile b/Makefile -index 53e5c5b..a2d3feb 100644 ---- a/Makefile -+++ b/Makefile -@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o - all: $(PROGS) tRNAscan-SE setpaths - - covels-SE: $(OBJ) scan_main.o -- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) -+ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) - - coves-SE: $(OBJ) score_main.o -- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) -+ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) - - eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o -- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \ -+ $(CC) $(CFLAGS) $(LDFLAGS) -o eufindtRNA eufind_main.o \ - pavesi.o $(SQUIDOBJ) $(LIBS) - - trnascan-1.4: trnascan.o -- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c -+ $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c - - tRNAscan-SE: - $(PERLDIR)/$(PERLBIN) checkversion.pl diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch new file mode 100644 index 000000000000..acf3c2a6d862 --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch @@ -0,0 +1,140 @@ +--- a/Makefile ++++ b/Makefile +@@ -20,9 +20,9 @@ + PERLBIN = perl + + ## where you want things installed +-BINDIR = $(HOME)/bin +-LIBDIR = $(HOME)/lib/tRNAscan-SE +-MANDIR = $(HOME)/man ++BINDIR = $(EPREFIX)/usr/bin ++LIBDIR = $(EPREFIX)/usr/share/trnascan-se ++MANDIR = $(EPREFIX)/usr/share/man + + ## NOTE !! If you later manually move the location of + ## binaries or data files in the BINDIR or LIBDIR directories, +@@ -33,10 +33,8 @@ + TEMPDIR = /tmp + + ## your compiler +-CC = gcc # GNU cc (if available) otherwise use vendor's cc + + ## any special compiler flags you want +-CFLAGS = -O # ok for most machines (remove -O for DEC OSF/1 cc compiler) + + ## machine specific definitions + # You shouldn't need any. The specific #define's in squid are historical. +@@ -58,7 +56,7 @@ + ####### + + SHELL = /bin/sh +-LIBS = -lm ++LIBS += -lm + .SUFFIXES : .c .o + + DOCS = README MANUAL INSTALL COPYING GNULICENSE FILES Release.history +@@ -109,20 +107,20 @@ + all: $(PROGS) tRNAscan-SE setpaths + + covels-SE: $(OBJ) scan_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) + + coves-SE: $(OBJ) score_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) + + eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o +- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \ ++ $(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA eufind_main.o \ + pavesi.o $(SQUIDOBJ) $(LIBS) + +-trnascan-1.4: trnascan.o +- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c ++trnascan-1.4: trnascan.c ++ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c + + tRNAscan-SE: +- $(PERLDIR)/$(PERLBIN) checkversion.pl ++ $(PERLBIN) checkversion.pl + sed 's#/tmp#$(TEMPDIR)#g' tRNAscan-SE.src | \ + sed 's#bindir = ""#bindir =\"$(BINDIR)/"#g' | \ + sed 's#/usr/local/lib/tRNAscanSE#$(LIBDIR)#g' | \ +@@ -200,11 +198,11 @@ + noambig: trnascan-1.4-NA eufindtRNA-NA + + trnascan-1.4-NA: trnascan.o +- $(CC) $(CFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c ++ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c + + eufindtRNA-NA: $(SQUIDOBJ) eufind_main.o +- $(CC) $(CFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c +- $(CC) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \ ++ $(CC) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c ++ $(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \ + pavesi-NA.o $(SQUIDOBJ) $(LIBS) + + +@@ -220,7 +218,7 @@ + rmdir -ps $(MANDIR) + + .c.o: +- $(CC) $(CFLAGS) $(MDEFS) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $< + + ## programs from Sean Eddy's sequence i/o function library not + ## needed for tRNAscan-SE but included for their utility +@@ -233,16 +231,16 @@ + cp $(UTILS) $(BINDIR)/. + + reformat: $(SQUIDOBJ) reformat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS) + + revcomp: $(SQUIDOBJ) revcomp_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS) + + seqstat: $(SQUIDOBJ) seqstat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS) + + shuffle: $(SQUIDOBJ) shuffle_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS) + + ## other programs in Cove package (below) not needed for + ## tRNAscan-SE, but are included for users who wish to apply +@@ -255,25 +253,25 @@ + cp $(COVE_SUITE) $(BINDIR)/. + + covea: $(OBJ) align_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS) + + coveb: $(OBJ) build_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS) + + covee: $(OBJ) emit_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS) + + covet: $(OBJ) train_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS) + + covels: $(OBJ) scan_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS) + + coves: $(OBJ) score_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS) + + structcheck: $(OBJ) structcheck_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS) + + + ## Maspar memory limits diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-portable-perl-shebangs.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-portable-perl-shebangs.patch new file mode 100644 index 000000000000..187705e8b3a0 --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-portable-perl-shebangs.patch @@ -0,0 +1,32 @@ +--- a/fasta2gsi.pl ++++ b/fasta2gsi.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Usage: fasta2gsi.perl <seqfile> + # Creates seqfile.gsi +--- a/instman.pl ++++ b/instman.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Sean Eddy, Wed Jul 29 15:24:43 1992 + +--- a/sstofa.pl ++++ b/sstofa.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + + if ($#ARGV < 0) { +--- a/tRNAscan-SE.src ++++ b/tRNAscan-SE.src +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + # + # -------------------------------------------------------------------- + # tRNAscan-SE: a program for improved detection of transfer RNA diff --git a/sci-biology/trnascan-se/metadata.xml b/sci-biology/trnascan-se/metadata.xml index 39da31794ca8..00b47df661a7 100644 --- a/sci-biology/trnascan-se/metadata.xml +++ b/sci-biology/trnascan-se/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild new file mode 100644 index 000000000000..f43243921f2f --- /dev/null +++ b/sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic perl-functions toolchain-funcs + +DESCRIPTION="tRNA detection in large-scale genome sequences" +HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/" +SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}"/tRNAscan-SE-1.3.1/ + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-lang/perl:=" +BDEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-portable-perl-shebangs.patch + "${FILESDIR}"/${P}-clang16.patch +) + +src_configure() { + tc-export CC + append-cflags -std=gnu89 # mid-migration from K&R C, incompatible with c2x +} + +src_test() { + emake PATH="${S}:${PATH}" testrun +} + +src_install() { + dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4 + + newman tRNAscan-SE.man tRNAscan-SE.man.1 + dodoc MANUAL Manual.ps README Release.history + + insinto /usr/share/trnascan-se + doins *.cm gcode.* Dsignal TPCsignal + + perl_domodule -r tRNAscanSE +} diff --git a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild deleted file mode 100644 index cd8dc152d6d2..000000000000 --- a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit perl-functions toolchain-funcs - -DESCRIPTION="tRNA detection in large-scale genome sequences" -HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/" -SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="" - -S="${WORKDIR}"/tRNAscan-SE-1.3.1/ - -PATCHES=( - "${FILESDIR}"/${P}-ldflags.patch -) - -src_prepare() { - default - sed \ - -e "s:BINDIR = \$(HOME)/bin:BINDIR = ${EPREFIX}/usr/bin:" \ - -e "s:LIBDIR = \$(HOME)/lib/tRNAscan-SE:LIBDIR = ${EPRFIX}/usr/share/${PN}:" \ - -e "s:MANDIR = \$(HOME)/man:MANDIR = ${EPREFIX}/usr/share/man:" \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CFLAGS = -O:CFLAGS = ${CFLAGS}:" \ - -i Makefile || die - - perl_set_version -} - -src_test() { - emake PATH="${S}:${PATH}" testrun -} - -src_install() { - dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4 - - newman tRNAscan-SE.man tRNAscan-SE.man.1 - - dodoc MANUAL README Release.history - - insinto /usr/share/${PN}/ - doins *.cm gcode.* Dsignal TPCsignal - - dodoc Manual.ps - - insinto ${VENDOR_LIB} - doins -r tRNAscanSE -} |