commit: b81269020c6c9871a04e418126f005d78b479f28 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Tue Jan 5 14:17:06 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Tue Jan 5 18:01:27 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b8126902
sci-biology/reapr: drop package, latest update 2015, no longer compiles Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/reapr/files/fix_sort_samtools13.patch | 16 -- sci-biology/reapr/files/use_shared_libs.patch | 252 ---------------------- sci-biology/reapr/metadata.xml | 12 -- sci-biology/reapr/reapr-1.0.18.ebuild | 61 ------ 4 files changed, 341 deletions(-) diff --git a/sci-biology/reapr/files/fix_sort_samtools13.patch b/sci-biology/reapr/files/fix_sort_samtools13.patch deleted file mode 100644 index f009223ce..000000000 --- a/sci-biology/reapr/files/fix_sort_samtools13.patch +++ /dev/null @@ -1,16 +0,0 @@ -Description: adapt samtools sort usage to 1.3 syntax - Samtools 1.3 changed the syntax of the 'samtools sort' command, breaking - REAPR's smaltmap command in the process. - Discussed and forwarded to upstream in person, hence no URL. -Author: Sascha Steinbiss <[email protected]> ---- a/src/task_smaltmap.pl -+++ b/src/task_smaltmap.pl -@@ -155,7 +155,7 @@ - . " | $samtools view -S -T $assembly -b - > $raw_bam"; - - # sort the bam by coordinate --push @commands, "$samtools sort $raw_bam $raw_bam.sort"; -+push @commands, "$samtools sort $raw_bam -O bam -o $raw_bam.sort.bam"; - - # remove duplicates - push @commands, "$samtools rmdup $raw_bam.sort.bam $rmdup_bam"; diff --git a/sci-biology/reapr/files/use_shared_libs.patch b/sci-biology/reapr/files/use_shared_libs.patch deleted file mode 100644 index b748c7e6d..000000000 --- a/sci-biology/reapr/files/use_shared_libs.patch +++ /dev/null @@ -1,252 +0,0 @@ -Description: Use_shared_libs ---- a/src/Makefile -+++ b/src/Makefile -@@ -1,7 +1,6 @@ --BAMTOOLS_ROOT = $(CURDIR)/bamtools - CC = g++ --CFLAGS = -Wl,-rpath,$(BAMTOOLS_ROOT)/lib -Wall -O3 -I $(BAMTOOLS_ROOT)/include -L $(BAMTOOLS_ROOT)/lib --TABIX = tabix/tabix.o -L./tabix -ltabix -lz -+CFLAGS = -Wall -O3 -I /usr/include/bamtools -I /usr/include -+TABIX = -ltabix -lhts -lz - STATS_OBJS = trianglePlot.o coveragePlot.o fasta.o histogram.o utils.o - SCORE_OBJS = errorWindow.o utils.o histogram.o - BREAK_OBJS = fasta.o utils.o -@@ -35,46 +34,46 @@ - $(CC) $(CFLAGS) -c histogram.cpp - - utils.o: utils.cpp -- $(CC) $(CFLAGS) -lbamtools -c utils.cpp -+ $(CC) $(CFLAGS) -c utils.cpp - - task_stats: task_stats.o $(STATS_OBJS) -- $(CC) $(CFLAGS) task_stats.o $(STATS_OBJS) -lbamtools -o task_stats $(TABIX) -+ $(CC) $(CFLAGS) task_stats.o $(STATS_OBJS) -lbamtools $(TABIX) -o task_stats - - task_stats.o: task_stats.cpp $(STATS_OBJS) - $(CC) $(CFLAGS) -c task_stats.cpp - - task_score: task_score.o $(SCORE_OBJS) -- $(CC) $(CFLAGS) task_score.o $(SCORE_OBJS) -lbamtools -o task_score $(TABIX) -+ $(CC) -o task_score $(CFLAGS) task_score.o $(SCORE_OBJS) -lbamtools $(TABIX) - - task_score.o: task_score.cpp $(SCORE_OBJS) - $(CC) $(CFLAGS) -c task_score.cpp - - task_break: task_break.o $(BREAK_OBJS) -- $(CC) $(CFLAGS) task_break.o $(BREAK_OBJS) -lbamtools -o task_break $(TABIX) -+ $(CC) $(CFLAGS) task_break.o $(BREAK_OBJS) -lbamtools $(TABIX) -o task_break - - task_break.o: task_break.cpp $(BREAK_OBJS) - $(CC) $(CFLAGS) -c task_break.cpp - - bam2fragCov: bam2fragCov.o $(BAM2COV_OBJS) -- $(CC) $(CFLAGS) bam2fragCov.o $(BAM2COV_OBJS) -lbamtools -o bam2fragCov $(TABIX) -+ $(CC) $(CFLAGS) bam2fragCov.o $(BAM2COV_OBJS) $(TABIX) -lbamtools -o bam2fragCov - - bam2fragCov.o: bam2fragCov.cpp $(BAM2COV_OBJS) - $(CC) $(CFLAGS) -c bam2fragCov.cpp - - bam2insert: bam2insert.o $(BAM2INSERT_OBJS) -- $(CC) $(CFLAGS) bam2insert.o $(BAM2INSERT_OBJS) -lbamtools -o bam2insert $(TABIX) -+ $(CC) $(CFLAGS) bam2insert.o $(BAM2INSERT_OBJS) $(TABIX) -lbamtools -o bam2insert - - bam2insert.o: bam2insert.cpp $(BAM2INSERT_OBJS) - $(CC) $(CFLAGS) -c bam2insert.cpp - - bam2perfect: bam2perfect.o $(BAM2PERFECT_OBJS) -- $(CC) $(CFLAGS) bam2perfect.o $(BAM2PERFECT_OBJS) -lbamtools -o bam2perfect $(TABIX) -+ $(CC) $(CFLAGS) bam2perfect.o $(BAM2PERFECT_OBJS) $(TABIX) -lbamtools -o bam2perfect - - bam2perfect.o: bam2perfect.cpp $(BAM2PERFECT_OBJS) - $(CC) $(CFLAGS) -c bam2perfect.cpp - - bam2fcdEstimate: bam2fcdEstimate.o $(BAM2FCDESTIMATE_OBJS) -- $(CC) $(CFLAGS) bam2fcdEstimate.o $(BAM2FCDESTIMATE_OBJS) -lbamtools -o bam2fcdEstimate $(TABIX) -+ $(CC) $(CFLAGS) bam2fcdEstimate.o $(TABIX) $(BAM2FCDESTIMATE_OBJS) -o bam2fcdEstimate - - bam2fcdEstimate.o: bam2fcdEstimate.cpp $(BAM2FCDESTIMATE_OBJS) - $(CC) $(CFLAGS) -c bam2fcdEstimate.cpp -@@ -110,13 +109,13 @@ - $(CC) $(CFLAGS) -c scaff2contig.cpp - - task_gapresize: task_gapresize.o $(GAPRESIZE_OBJS) -- $(CC) $(CFLAGS) task_gapresize.o $(GAPRESIZE_OBJS) -lbamtools -o task_gapresize $(TABIX) -+ $(CC) $(CFLAGS) task_gapresize.o $(TABIX) $(GAPRESIZE_OBJS) -o task_gapresize - - task_gapresize.o: task_gapresize.cpp $(GAPRESIZE_OBJS) - $(CC) $(CFLAGS) -c task_gapresize.cpp - - task_fcdrate: task_fcdrate.o $(FCDRATE_OBJS) -- $(CC) $(CFLAGS) task_fcdrate.o $(FCDRATE_OBJS) -lbamtools -o task_fcdrate $(TABIX) -+ $(CC) $(CFLAGS) task_fcdrate.o $(TABIX) $(FCDRATE_OBJS) -o task_fcdrate - - task_fcdrate.o: task_fcdrate.cpp $(FCDRATE_OBJS) - $(CC) $(CFLAGS) -c task_fcdrate.cpp ---- a/src/task_break.cpp -+++ b/src/task_break.cpp -@@ -10,7 +10,6 @@ - #include <assert.h> - #include "fasta.h" - #include "utils.h" --#include "tabix/tabix.hpp" - - using namespace std; - ---- a/src/task_score.cpp -+++ b/src/task_score.cpp -@@ -18,7 +18,6 @@ - #include "histogram.h" - #include "api/BamMultiReader.h" - #include "api/BamReader.h" --#include "tabix/tabix.hpp" - - using namespace BamTools; - using namespace std; ---- a/src/task_stats.cpp -+++ b/src/task_stats.cpp -@@ -18,7 +18,6 @@ - #include "utils.h" - #include "api/BamMultiReader.h" - #include "api/BamReader.h" --#include "tabix/tabix.hpp" - - using namespace BamTools; - using namespace std; ---- a/src/utils.h -+++ b/src/utils.h -@@ -11,7 +11,7 @@ - - #include "api/BamMultiReader.h" - #include "api/BamReader.h" --#include "tabix/tabix.hpp" -+#include "tabix.hpp" - - const short INNIE = 1; - const short OUTTIE = 2; ---- a/src/task_fcdrate.cpp -+++ b/src/task_fcdrate.cpp -@@ -9,7 +9,6 @@ - - #include "utils.h" - #include "histogram.h" --#include "tabix/tabix.hpp" - - using namespace std; - ---- a/src/reapr.pl -+++ b/src/reapr.pl -@@ -12,8 +12,8 @@ - $this_script = File::Spec->rel2abs($this_script); - my ($scriptname, $scriptdir) = fileparse($this_script); - $scriptdir = File::Spec->rel2abs($scriptdir); --my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix'); --my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip'); -+my $tabix = 'tabix'; -+my $bgzip = 'bgzip'; - my $version = '1.0.18'; - - if ($#ARGV == -1) { ---- a/src/task_preprocess.pl -+++ b/src/task_preprocess.pl -@@ -52,9 +52,9 @@ - my $ideal_fcd_file = File::Spec->catfile($sample_dir, 'ideal_fcd.txt'); - my $lowess_prefix = File::Spec->catfile($sample_dir, 'gc_vs_cov.lowess'); - my $r_script = File::Spec->catfile($sample_dir, 'gc_vs_cov.R'); --my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix'); --my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip'); --my $samtools = File::Spec->catfile($scriptdir, 'samtools'); -+my $tabix = 'tabix'; -+my $bgzip = 'bgzip'; -+my $samtools = 'samtools'; - - # make directory and soft links to required files - $fasta_in = File::Spec->rel2abs($fasta_in); ---- a/src/task_perfectfrombam.pl -+++ b/src/task_perfectfrombam.pl -@@ -57,12 +57,12 @@ - my $min_perfect_map_qual = $ARGV[5]; - my $min_align_score = $ARGV[6]; - my $bam2perfect = File::Spec->catfile($scriptdir, 'bam2perfect'); --my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip'); --my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix'); -+my $bgzip = 'bgzip'; -+my $tabix = 'tabix'; - my $ERROR_PREFIX = '[REAPR perfectfrombam]'; - my $perfect_bam = "$out_prefix.tmp.perfect.bam"; - my $repetitive_bam = "$out_prefix.tmp.repetitive.bam"; --my $samtools = File::Spec->catfile($scriptdir, 'samtools'); -+my $samtools = 'samtools'; - my %seq_lengths; - my %used_seqs; - my $hist_file = "$out_prefix.hist"; ---- a/src/task_perfectmap.pl -+++ b/src/task_perfectmap.pl -@@ -38,14 +38,14 @@ - my $reads_2 = $ARGV[2]; - my $fragsize = $ARGV[3]; - my $preout = $ARGV[4]; --my $findknownsnps = File::Spec->catfile($scriptdir, 'findknownsnps'); -+my $findknownsnps = 'findknownsnps'; - my $ERROR_PREFIX = '[REAPR perfect_map]'; - my $raw_coverage_file = "$preout.tmp.cov.txt"; - my $tmp_bin = "$preout.tmp.bin"; - my $tmp_bin_single_match = "$tmp_bin\_single_match.fastq"; --my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix'); --my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip'); --my $samtools = File::Spec->catfile($scriptdir, 'samtools'); -+my $tabix = 'tabix'; -+my $bgzip = 'bgzip'; -+my $samtools = 'samtools'; - my $all_bases_outfile = "$preout.perfect_cov.gz"; - my $hist_outfile = "$preout.hist"; - my @coverage = (0) x 101; ---- a/src/task_plots.pl -+++ b/src/task_plots.pl -@@ -50,9 +50,9 @@ - } - - --my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix'); --my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip'); --my $samtools = File::Spec->catfile($scriptdir, 'samtools'); -+my $tabix = 'tabix'; -+my $bgzip = 'bgzip'; -+my $samtools = 'samtools'; - my @plot_list = ('frag_cov', 'frag_cov_cor', 'read_cov', 'read_ratio_f', 'read_ratio_r', 'clip', 'FCD_err'); - my @file_list; - my $fa_out = "$outprefix.ref.fa"; ---- a/src/task_pipeline.pl -+++ b/src/task_pipeline.pl -@@ -9,7 +9,7 @@ - - my ($scriptname, $scriptdir) = fileparse($0); - my $reapr_dir = abs_path(File::Spec->catfile($scriptdir, File::Spec->updir())); --my $reapr = File::Spec->catfile($reapr_dir, 'reapr'); -+my $reapr = 'reapr'; - - my %options = (fcdcut => 0); - ---- a/src/task_seqrename.pl -+++ b/src/task_seqrename.pl -@@ -7,7 +7,7 @@ - use Getopt::Long; - - my ($scriptname, $scriptdir) = fileparse($0); --my $samtools = File::Spec->catfile($scriptdir, 'samtools'); -+my $samtools = 'samtools'; - my %options; - my $usage = qq/<rename file> <in.bam> <out.bam> - ---- a/src/task_smaltmap.pl -+++ b/src/task_smaltmap.pl -@@ -77,8 +77,8 @@ - my $reads_2 = $ARGV[2]; - my $final_bam = $ARGV[3]; - my $ERROR_PREFIX = '[REAPR smaltmap]'; --my $samtools = File::Spec->catfile($scriptdir, 'samtools'); --my $smalt = File::Spec->catfile($scriptdir, 'smalt'); -+my $samtools = 'samtools'; -+my $smalt = 'smalt'; - my $tmp_prefix = "$final_bam.tmp.$$.smaltmap"; - my $smalt_index = "$tmp_prefix.smalt_index"; - my $smalt_sample = "$tmp_prefix.smalt_sample"; diff --git a/sci-biology/reapr/metadata.xml b/sci-biology/reapr/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/reapr/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/reapr/reapr-1.0.18.ebuild b/sci-biology/reapr/reapr-1.0.18.ebuild deleted file mode 100644 index a8c226c9d..000000000 --- a/sci-biology/reapr/reapr-1.0.18.ebuild +++ /dev/null @@ -1,61 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit eutils - -DESCRIPTION="Verify and correct genome assembly scaffolds using paired-end reads" -HOMEPAGE="http://www.sanger.ac.uk/science/tools/reapr"; -SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_${PV}.tar.gz - ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_1.0.18.manual.pdf"; - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" -IUSE="" - -# tested smalt versions 0.6.4 to 0.7.0.1 only -DEPEND="sci-biology/bamtools - =sci-biology/samtools-0.1.19-r2" # actually bundled is 0.1.18 -RDEPEND="${DEPEND}" -# sci-biology/smalt -# dev-perl/File-Basename -# dev-perl/File-Copy -# dev-perl/File-Spec -# perl-core/Getopt-Long -# dev-perl/List-Util -# dev-lang/R" - -S="${WORKDIR}"/Reapr_"${PV}" - -# we use temporarily patches from https://anonscm.debian.org/cgit/debian-med/reapr.git/tree/debian/patches - -src_prepare(){ - default - for f in "${FILESDIR}"/*.patch; do epatch $f || die; done - sed -e 's#^CC = g++#CXX ?= g++#' -i src/Makefile || die - sed -e 's#$(CC)#$(CXX)#' -i src/Makefile || die - sed -e 's#-O3##' -i src/Makefile || die - sed -e 's#^CFLAGS =#CXXFLAGS += -I../third_party/tabix -L../third_party/tabix -I../third_party/bamtools/src -L../third_party/bamtools/src#' -i src/Makefile || die - #sed -e 's#-lbamtools#../third_party/bamtools/src/libbamtools.so#' -i src/Makefile || die - sed -e 's#-ltabix#../third_party/tabix/libtabix.a#' -i src/Makefile || die - sed -e 's#CFLAGS#CXXFLAGS#' -i src/Makefile || die -} - -src_compile(){ - cd third_party/tabix || die - emake # to yield tabix.o object - cd ../.. || die - cd src || die - emake # link directly tabix.o but elsewhere also ../third_party/tabix/libtabix.a -} - -src_install(){ - dodoc "${DISTDIR}"/Reapr_"${PV}".manual.pdf -} - -pkg_postinst(){ - einfo "There are test data at ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_${PV}.test_data.tar.gz"; - einfo "You can view results with >=sci-biology/artemis*-15.0.0" -}
