[med-svn] [reapr] 01/02: correct paths to tabix/bgzip

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository reapr.

commit 39b9db9336cbcc2ba3402af4579fa5d1c7ad5aed
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Sun Dec 13 19:35:13 2015 +0000

    correct paths to tabix/bgzip
---
 debian/patches/use_shared_libs | 76 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 76 insertions(+)

diff --git a/debian/patches/use_shared_libs b/debian/patches/use_shared_libs
index 1f1d009..2090649 100644
--- a/debian/patches/use_shared_libs
+++ b/debian/patches/use_shared_libs
@@ -133,3 +133,79 @@ Description: Use_shared_libs
  
  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 $tabix = File::Spec->catfile($scriptdir, 'tabix');
++my $bgzip = File::Spec->catfile($scriptdir, 'bgzip');
+ my $version = '1.0.18';
+ 
+ if ($#ARGV == -1) {
+--- a/src/task_preprocess.pl
++++ b/src/task_preprocess.pl
+@@ -52,8 +52,8 @@
+ 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 $tabix = File::Spec->catfile($scriptdir, 'tabix');
++my $bgzip = File::Spec->catfile($scriptdir, 'bgzip');
+ my $samtools = File::Spec->catfile($scriptdir, 'samtools');
+ 
+ # make directory and soft links to required files
+--- a/src/task_perfectfrombam.pl
++++ b/src/task_perfectfrombam.pl
+@@ -57,8 +57,8 @@
+ 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 $bgzip = File::Spec->catfile($scriptdir, 'bgzip');
++my $tabix = File::Spec->catfile($scriptdir, 'tabix');
+ my $ERROR_PREFIX = '[REAPR perfectfrombam]';
+ my $perfect_bam = "$out_prefix.tmp.perfect.bam";
+ my $repetitive_bam = "$out_prefix.tmp.repetitive.bam";
+--- a/src/task_perfectmap.pl
++++ b/src/task_perfectmap.pl
+@@ -43,8 +43,8 @@
+ 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 $tabix = File::Spec->catfile($scriptdir, 'tabix');
++my $bgzip = File::Spec->catfile($scriptdir, 'bgzip');
+ my $samtools = File::Spec->catfile($scriptdir, 'samtools');
+ my $all_bases_outfile = "$preout.perfect_cov.gz";
+ my $hist_outfile = "$preout.hist";
+--- a/src/task_plots.pl
++++ b/src/task_plots.pl
+@@ -50,8 +50,8 @@
+ }
+ 
+ 
+-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
+-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
++my $tabix = File::Spec->catfile($scriptdir, 'tabix');
++my $bgzip = File::Spec->catfile($scriptdir, 'bgzip');
+ my $samtools = File::Spec->catfile($scriptdir, 'samtools');
+ my @plot_list = ('frag_cov', 'frag_cov_cor', 'read_cov', 'read_ratio_f', 'read_ratio_r', 'clip', 'FCD_err');
+ my @file_list;
+--- 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 = '/usr/bin/reapr';
+ 
+ my %options = (fcdcut => 0);
+ 

-- 
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