Mercurial > repos > joachim-jacob > qualimap_suite

comparison bamqc_wrapper.pl @ 4:3d690162d629 draft

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Added more details for the required dependencies.
author Joachim Jacob <joachim.jacob@gmail.com>
date Wed, 20 Mar 2013 09:35:07 +0100
parents 934cd08c77af
children
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3:9537dd9dd18b 4:3d690162d629
63 63
64 my $tempdir = File::Temp->tempdir('tmpXXXXX', DIR => $galtemp, CLEANUP => 1); 64 my $tempdir = File::Temp->tempdir('tmpXXXXX', DIR => $galtemp, CLEANUP => 1);
65 mkdir "$tempdir", 077 unless -d "$tempdir"; 65 mkdir "$tempdir", 077 unless -d "$tempdir";
66 INFO "\nTemporary directory:\n$tempdir"; 66 INFO "\nTemporary directory:\n$tempdir";
67 67
68
69 # ---------------------- Output files ---------------------------------#
70 ########################################################################
71 # Two possible scenarios
72 # - output is written to the file at the output location in config file
73 # - output is moved to the output file location
74
75 # open (SAMOUTPUT, ">$para{'output_sam'}")
76 # or ( ERROR "Could not open output file for writing! (file:$para{'output_sam'}" and die );
77 # print SAMOUTPUT "Here comes sam\n";
78 # close (SAMOUTPUT);
79
80
81 # -------------------- Assembling command ----------------------------# 68 # -------------------- Assembling command ----------------------------#
82 ######################################################################## 69 ########################################################################
83 my $outdir="bamqc_output"; 70 my $outdir="bamqc_output";
84 my $qualimap_path=""; # for tool_dependency later on 71 my $qualimap_path=""; # for tool_dependency later on
85 my $command = $qualimap_path."qualimap bamqc --outdir $outdir"; # this will ultimately be executed 72 my $command = $qualimap_path."qualimap bamqc --outdir $outdir"; # this will ultimately be executed