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* [gentoo-commits] proj/sci:master commit in: sci-biology/reapr/files/, sci-biology/reapr/
@ 2016-03-31 22:52 Martin Mokrejs
  0 siblings, 0 replies; 2+ messages in thread
From: Martin Mokrejs @ 2016-03-31 22:52 UTC (permalink / raw
  To: gentoo-commits

commit:     c2774f23f13407f20176e96d3c85d8918c8ca9c1
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 31 22:50:10 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 31 22:50:10 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c2774f23

sci-biology/reapr: quick and dirty Debian patches do not help me with sci-biology/bamtools-2.3.0 installed site-wide; the bundled bamtools do not start to compile and tehrefore reapr linking steps fail while using using system-wide incompatible version

Package-Manager: portage-2.2.28

 sci-biology/reapr/files/fix_sort_samtools13.patch |  16 ++
 sci-biology/reapr/files/use_shared_libs.patch     | 252 ++++++++++++++++++++++
 sci-biology/reapr/reapr-1.0.18.ebuild             |  12 +-
 3 files changed, 277 insertions(+), 3 deletions(-)

diff --git a/sci-biology/reapr/files/fix_sort_samtools13.patch b/sci-biology/reapr/files/fix_sort_samtools13.patch
new file mode 100644
index 0000000..f009223
--- /dev/null
+++ b/sci-biology/reapr/files/fix_sort_samtools13.patch
@@ -0,0 +1,16 @@
+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 <sascha@steinbiss.name>
+--- 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
new file mode 100644
index 0000000..b748c7e
--- /dev/null
+++ b/sci-biology/reapr/files/use_shared_libs.patch
@@ -0,0 +1,252 @@
+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/reapr-1.0.18.ebuild b/sci-biology/reapr/reapr-1.0.18.ebuild
index 312219a..893af8b 100644
--- a/sci-biology/reapr/reapr-1.0.18.ebuild
+++ b/sci-biology/reapr/reapr-1.0.18.ebuild
@@ -2,7 +2,9 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
+
+inherit eutils
 
 DESCRIPTION="Verify and correct genome assembly scaffolds using paired-end reads"
 HOMEPAGE="http://www.sanger.ac.uk/science/tools/reapr"
@@ -11,7 +13,7 @@ SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_${PV}.tar.gz
 
 LICENSE="GPL-3"
 SLOT="0"
-KEYWORDS="" # does not link against -lbamtools
+KEYWORDS=""
 IUSE=""
 
 # tested smalt versions 0.6.4 to 0.7.0.1 only
@@ -28,11 +30,15 @@ RDEPEND="${DEPEND}"
 
 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/bamtools/src -L../third_party/bamtools/src#' -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


^ permalink raw reply related	[flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/reapr/files/, sci-biology/reapr/
@ 2021-01-05 18:05 Andrew Ammerlaan
  0 siblings, 0 replies; 2+ messages in thread
From: Andrew Ammerlaan @ 2021-01-05 18:05 UTC (permalink / raw
  To: gentoo-commits

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 <sascha@steinbiss.name>
---- 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>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</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"
-}


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2016-03-31 22:52 [gentoo-commits] proj/sci:master commit in: sci-biology/reapr/files/, sci-biology/reapr/ Martin Mokrejs
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2021-01-05 18:05 Andrew Ammerlaan

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