# HG changeset patch # User Franco Caramia # Date 1401780688 -36000 # Node ID c361b3fb806ec7722de32365fe38b6eb79baaa9f # Parent 6bcf47cc272a8ca703cedc177624cc646bfea0d4 added Nicola Path 2.0 diff -r 6bcf47cc272a -r c361b3fb806e contra.xml --- a/contra.xml Mon May 19 20:00:44 2014 -0400 +++ b/contra.xml Tue Jun 03 17:31:28 2014 +1000 @@ -2,8 +2,10 @@ : Copy Number Analysis for Targeted Resequencing bedtools - samtools - contra + samtools + R + contra + diff -r 6bcf47cc272a -r c361b3fb806e contra_wrapper.pl --- a/contra_wrapper.pl Mon May 19 20:00:44 2014 -0400 +++ b/contra_wrapper.pl Tue Jun 03 17:31:28 2014 +1000 @@ -1,7 +1,7 @@ use strict; use warnings; -use FindBin; +use Find; use File::Path qw(make_path); use File::Spec; @@ -22,7 +22,7 @@ { my $variable = $tmp[1]; $variable =~ s/=/ /g; - print "$variable\n"; + $player_options = "$player_options $variable"; } elsif($tmp[0] eq "CONTRAOUTPUT") @@ -40,52 +40,28 @@ } -my $working_dir = "CONTRA_OUTPUT"; + +my $working_dir = File::Spec->catfile($contra_dir, 'CONTRA_OUTPUT'); make_path($contra_dir); #remove extension -#run contra -system(File::Spec->catfile($FindBin::Bin, 'contra.py') . " -o $working_dir $player_options > /dev/null 2>&1"); +my $cmd = "contra.py -o $working_dir $player_options"; +print "Command to be executed: $cmd\n"; +system($cmd); #set html #print "$contra_output - $working_dir\n"; open(HTML, ">$contra_output"); print HTML "Contra: Copy Number Analysis for Targeted Resequencing

Contra Output Files:

\n"; close(HTML); -sub move_files -{ - my $local_dir = $_[0]; - opendir(DIR, $local_dir); - #print ("Openning: $local_dir\n"); - my @FILES= readdir(DIR); - closedir(DIR); - foreach my $file (@FILES) - { - if ($file eq "." || $file eq "..") - { - #print ("./ or ../ skipped\n"); - } - elsif (-d "$local_dir/$file") - { - #print ("moving to: $local_dir/$file\n"); - move_files("$local_dir/$file"); - } - elsif (-f "$local_dir/$file") - { - #print ("mv $local_dir/$file $contra_dir\n"); - print HTML "
  • $file
    • \n"; - system ("mv $local_dir/$file $contra_dir"); - } - else - { - die("Unrecognized file generated: $file\n"); - } - - - } - +sub add_file { + if (-f $File::Find::name) { + my $rel_path = File::Spec->abs2rel($File::Find::name, $working_dir); + print ("adding $rel_path\n"); + print HTML "
  • $rel_path
    • \n"; + } } diff -r 6bcf47cc272a -r c361b3fb806e tool_dependencies.xml --- a/tool_dependencies.xml Mon May 19 20:00:44 2014 -0400 +++ b/tool_dependencies.xml Tue Jun 03 17:31:28 2014 +1000 @@ -1,44 +1,28 @@ + + + + + - - - http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2 - sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile - make - - samtools - $INSTALL_DIR/bin - - - misc/maq2sam-long - $INSTALL_DIR/bin - - - $INSTALL_DIR/bin - - - - - Compiling SAMtools requires the ncurses and zlib development libraries. - + - - - http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz - make all - $INSTALL_DIR/bin - - bin - $INSTALL_DIR/bin - - - $INSTALL_DIR/bin - - + + http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz + make all + $INSTALL_DIR/bin + + bin + $INSTALL_DIR/bin + + + $INSTALL_DIR/bin + + GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools. g++ required @@ -48,13 +32,7 @@ http://downloads.sourceforge.net/project/contra-cnv/CONTRA.V2.0/CONTRA.v2.0.4.tar.gz - rm -rf bedtools_installation_guide.txt - rm -rf BEDTools-User-Manual.v4.pdf - rm -rf BEDTools.v2.11.2.tar.gz - rm -rf CONTRA_User_Guide.2.0.pdf - $INSTALL_DIR/bin - $INSTALL_DIR/bin/scripts - + contra.py $INSTALL_DIR/bin @@ -62,7 +40,7 @@ baseline.py $INSTALL_DIR/bin - + scripts $INSTALL_DIR/bin/scripts