Author: Andreas Tille <tille@debian.org>
Last-Update: Sat, 06 Oct 2018 11:09:26 +0200
Description: Adapt scripts to Debian installation

--- a/plasmidseeker.pl
+++ b/plasmidseeker.pl
@@ -13,7 +13,7 @@
 my $glistquery = "/usr/bin/glistquery";
 my $glistcompare = "/usr/bin/glistcompare";
 my $gdistribution = "/usr/bin/gdistribution";
-my $rtest = "$FindBin::RealBin/testfunction.R";
+my $rtest = "/usr/share/plasmidseeker/testfunction.R";
 
 # INPUT FILES AND NAMES
 my @input_files; # Input fastas
--- a/plasmidseeker_ecoli_test.sh
+++ b/plasmidseeker_ecoli_test.sh
@@ -1,14 +1,6 @@
 #!bin/bash
 #Script for testing plasmid identification from E. coli WGS samples
 
-chmod 755 GenomeTester4/glistquery
-chmod 755 GenomeTester4/glistmaker
-chmod 755 GenomeTester4/glistcompare
-chmod 755 GenomeTester4/gdistribution
-chmod 755 plasmidseeker.pl
-chmod 755 database_builder.pl
-chmod 755 testfunction.R
-
 #Download PlasmidSeeker database and E. coli files
 
 echo "Downloading PlasmidSeeker database..."
@@ -32,13 +24,13 @@
 #Use plamidseeker to identify E. coli samples
 
 echo "Identifying E. coli sample EC1"
-perl plasmidseeker.pl -d db_w20 -i ERR1937840.fastq -b e_coli_sakai_ref.fna -o EC_1_results.txt
+plasmidseeker -d db_w20 -i ERR1937840.fastq -b e_coli_sakai_ref.fna -o EC_1_results.txt
 
 echo "Identifying E. coli sample EC2"
-perl plasmidseeker.pl -d db_w20 -i ERR1937914.fastq -b e_coli_sakai_ref.fna -o EC_2_results.txt
+plasmidseeker -d db_w20 -i ERR1937914.fastq -b e_coli_sakai_ref.fna -o EC_2_results.txt
 
 echo "Identifying E. coli sample EC3"
-perl plasmidseeker.pl -d db_w20 -i ERR1937841.fastq -b e_coli_sakai_ref.fna -o EC_3_results.txt
+plasmidseeker -d db_w20 -i ERR1937841.fastq -b e_coli_sakai_ref.fna -o EC_3_results.txt
 
 echo "Removing temporary files..."
 rm tmp*