Mercurial > repos > davidvanzessen > mutation_analysis
comparison tmp/baseline/wrapper.sh @ 109:0096cd454380 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 14 Jul 2016 07:29:56 -0400 |
| parents | a66eb1c5374c |
| children |
comparison
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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 |