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 |
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| 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' ' '` |