diff options
Diffstat (limited to 'sci-biology/reapr/files/use_shared_libs.patch')
| -rw-r--r-- | sci-biology/reapr/files/use_shared_libs.patch | 252 |
1 files changed, 0 insertions, 252 deletions
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"; |