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comparison tmp/baseline/wrapper.sh @ 109:0096cd454380 draft

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author davidvanzessen
date Thu, 14 Jul 2016 07:29:56 -0400
parents a66eb1c5374c
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108:6add3e66f4fa 109:0096cd454380
75 else 75 else
76 python $dir/script_xlsx.py --input $current --ref $ref --output $fasta 76 python $dir/script_xlsx.py --input $current --ref $ref --output $fasta
77 fi 77 fi
78 count=$((count+1)) 78 count=$((count+1))
79 done 79 done
80
81 if [[ $(wc -l < $fasta) -eq "1" ]]; then
82 echo "No sequences in the fasta file, exiting"
83 exit 0
84 fi
85
80 workdir="$PWD" 86 workdir="$PWD"
81 cd $dir 87 cd $dir
82 echo "file: ${inputs[0]}" 88 echo "file: ${inputs[0]}"
83 #Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region ${inputs[0]} $workdir/ $outID 2>&1 89 #Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region ${inputs[0]} $workdir/ $outID 2>&1
84 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1 90 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1