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Last change
on this file since 2495 was
2495,
checked in by Nicklas Nordborg, 9 years ago
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Adding wrapper for calling trimmomatic. Includes default settings for memory and path to JAR file. Can be overridden by setting environment variables before calling the script. First parameter is the command (PE/SE), rest of parameters are forwarded to trimmomatic.
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File size:
307 bytes
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| 1 | #!/bin/sh |
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| 2 | |
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| 3 | if [ -z "$TrimmomaticJAR" ]; then |
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| 4 | TrimmomaticJAR=/usr/local/packages/trimmomatic/0.32/trimmomatic-0.32.jar |
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| 5 | fi |
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| 6 | |
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| 7 | if [ -z "$TrimmomaticMemory" ]; then |
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| 8 | TrimmomaticMemory=16g |
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| 9 | fi |
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| 10 | |
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| 11 | NumThreads=`nproc` |
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| 12 | |
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| 13 | cmd=$1 |
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| 14 | shift |
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| 15 | |
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| 16 | java -Xmx${TrimmomaticMemory} -jar ${TrimmomaticJAR} ${cmd} -threads ${NumThreads} $@ |
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