annotate trimmomatic.sh @ 2:a60283899c6d
draft
Version 0.32.2: use GALAXY_SLOTS to set number of threads.
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pjbriggs |
| date |
Wed, 22 Apr 2015 09:36:27 -0400 |
| parents |
3358c3d30143 |
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0
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1 #!/bin/sh
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2 #
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3 # Shell wrapper to run Trimmomatic jar file as a Galaxy tool
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4 echo Arguments:
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5 for i in $@ ; do
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6 echo "*" $i
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7 done
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8 java $@ 2>&1 | tee trimmomatic.log
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9 status=$?
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10 echo "Exit status: $status"
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11 # Check for successful completion
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12 if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ] ; then
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13 echo "Trimmomatic did not finish successfully" >&2
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14 exit 1
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15 fi
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16 exit $status
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17 ##
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18 #
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