[med-svn] [trinityrnaseq] 01/03: add patch to cope with path changes

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository trinityrnaseq.

commit d188754939f84066e2bfcb7c503a40f09a9960ef
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Wed Sep 16 10:37:16 2015 -0700

    add patch to cope with path changes
---
 debian/patches/fix_system_paths | 81 +++++++++++++++++++++++++++++++++++++++++
 debian/patches/series           |  1 +
 2 files changed, 82 insertions(+)

diff --git a/debian/patches/fix_system_paths b/debian/patches/fix_system_paths
new file mode 100644
index 0000000..0464241
--- /dev/null
+++ b/debian/patches/fix_system_paths
@@ -0,0 +1,81 @@
+Description: drop some use of FindBin and hardcode paths
+Author: Tim Booth <tbooth at ceh.ac.uk>
+--- a/util/align_and_estimate_abundance.pl
++++ b/util/align_and_estimate_abundance.pl
+@@ -2,15 +2,14 @@
+ 
+ use strict;
+ use warnings;
+-use FindBin;
+ 
+ use Cwd;
+ 
+ use Getopt::Long qw(:config no_ignore_case bundling pass_through);
+ 
+ 
+-my $RSEM_DIR = "$FindBin::Bin/../trinity-plugins/rsem";
+-$ENV{PATH} = "$RSEM_DIR:$ENV{PATH}"; # be sure to use the included rsem package over other ones installed.
++my $DM_DIR = "/usr/lib/debian-med/bin";
++$ENV{PATH} = "$DM_DIR:$ENV{PATH}"; # be sure to find the right express executable
+ 
+ 
+ my %aligner_params = ( 'bowtie_RSEM' => '--all --best --strata -m 300 --chunkmbs 512',
+@@ -352,7 +351,7 @@
+ 
+     if ($trinity_mode && ! $gene_trans_map_file) {
+         $gene_trans_map_file = "$transcripts.gene_trans_map";
+-        my $cmd = "$FindBin::Bin/support_scripts/get_Trinity_gene_to_trans_map.pl $transcripts > $gene_trans_map_file";
++        my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl '$transcripts' > '$gene_trans_map_file'";
+         &process_cmd($cmd) unless (-e $gene_trans_map_file);
+     }
+         
+@@ -576,7 +575,7 @@
+ sub make_eXpress_genes_file {
+     my ($results_xprs_file, $gene_to_trans_map_file) = @_;
+ 
+-    my $cmd = "$FindBin::Bin/support_scripts/eXpress_trans_to_gene_results.pl $results_xprs_file $gene_to_trans_map_file > $results_xprs_file.genes";
++    my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/eXpress_trans_to_gene_results.pl '$results_xprs_file' '$gene_to_trans_map_file' > '$results_xprs_file.genes'";
+     &process_cmd($cmd);
+     
+     return;
+--- a/Trinity
++++ b/Trinity
+@@ -5,8 +5,7 @@
+ use threads;
+ no strict qw(subs refs);
+ 
+-use FindBin;
+-use lib ("$FindBin::Bin/PerlLib");
++use lib ("/usr/lib/trinityrnaseq/PerlLib");
+ use File::Basename;
+ use Time::localtime;
+ use Cwd;
+@@ -22,7 +21,7 @@
+ 
+ BEGIN {
+ 
+-    $ENV{TRINITY_HOME} = "$FindBin::Bin";
++    $ENV{TRINITY_HOME} = "/usr/lib/trinityrnaseq";
+ 
+ }
+ 
+@@ -440,7 +439,7 @@
+ #        Trinity --genome_guided_bam rnaseq_alignments.csorted.bam --max_memory 50G\
+ #                --genome_guided_max_intron 10000 --CPU 6
+ #
+-#     see: $FindBin::RealBin/sample_data/test_Trinity_Assembly/
++#     see: /usr/lib/trinityrnaseq/sample_data/test_Trinity_Assembly/
+ #          for sample data and 'runMe.sh' for example Trinity execution
+ #
+ #     For more details, visit: http://trinityrnaseq.github.io
+--- a/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
++++ b/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
+@@ -8,7 +8,7 @@
+ use FindBin;
+ use File::Basename;
+ 
+-$ENV{PATH} .= ":$FindBin::Bin/../../trinity-plugins/slclust/bin/";
++$ENV{PATH} .= ":/usr/lib/trinityrnaseq/trinity-plugins/slclust/bin/";
+ 
+ my $help_flag;
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 0f88e83..7daf669 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -6,3 +6,4 @@ collections15-to-4
 0001-fix_gcc5.patch.patch
 0002-fix_istream_failure_call.patch
 fix-jsquery
+fix_system_paths

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trinityrnaseq.git