Mercurial > repos > joachim-jacob > qualimap_suite
comparison bamqc_wrapper.pl @ 4:3d690162d629 draft
Added more details for the required dependencies.
author | Joachim Jacob <joachim.jacob@gmail.com> |
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date | Wed, 20 Mar 2013 09:35:07 +0100 |
parents | 934cd08c77af |
children |
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3:9537dd9dd18b | 4:3d690162d629 |
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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 |