Mercurial > repos > davidvanzessen > baseline_bayesian_estimation

comparison wrapper.sh @ 8:525b58fc8622 draft

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author davidvanzessen
date Tue, 02 Jun 2015 05:02:23 -0400
parents 45a5e3bd9df4
children e160483ee900
comparison
equal deleted inserted replaced
7:45a5e3bd9df4 8:525b58fc8622
66 fi 66 fi
67 count=$((count+1)) 67 count=$((count+1))
68 done 68 done
69 workdir="$PWD" 69 workdir="$PWD"
70 cd $dir 70 cd $dir
71 echo "file: ${inputs[0]}"
72 #Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region ${inputs[0]} $workdir/ $outID 2>&1
71 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1 73 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1
72 74
73 echo "$workdir/${outID}.txt" 75 echo "$workdir/${outID}.txt"
74 76
75 rows=`tail -n +2 $workdir/${outID}.txt | grep -v "All sequences combined" | grep -n 'Group' | grep -Eoh '^[0-9]+' | tr '\n' ' '` 77 rows=`tail -n +2 $workdir/${outID}.txt | grep -v "All sequences combined" | grep -n 'Group' | grep -Eoh '^[0-9]+' | tr '\n' ' '`