Mercurial > repos > sanbi-uwc > trimmomatic

annotate trimmomatic_LOCAL_16925.sh @ 5:069b6b601fad draft default tip

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planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 779c2af9e413bd7098662231d07e6b857161f48d
author sanbi-uwc
date Mon, 23 Jan 2017 07:53:06 -0500
parents 642a39a927c9
children
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642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
parents:
diff changeset
1 #!/bin/sh
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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2 #
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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3 # Shell wrapper to run Trimmomatic jar file as a Galaxy tool
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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4 echo Arguments:
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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5 for i in $@ ; do
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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6 echo "*" $i
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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7 done
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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8
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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9 if [ -n "$CONDA_PREFIX" ] ; then
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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10 # bioconda installs trimmomatic in a share directory
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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11 # with a jarfile called trimmomatic.jar
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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12 TRIMMOMATIC_DIR="$CONDA_PREFIX/share/trimmomatic"
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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13 JARFILE="trimmomatic.jar"
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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14 else
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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15 JARFILE="trimmomatic-0.36.jar"
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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16 fi
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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17
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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18 if [ -z "$TRIMMOMATIC_DIR" ] ; then
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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19 echo "TRIMMOMATIC_DIR variable not set, can't find jar file"
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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20 exit 1
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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21 fi
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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22
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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23 java -mx16G -jar $TRIMMOMATIC_DIR/$JARFILE $@ 2>&1 | tee trimmomatic.log
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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24 status=$?
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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25 echo "Exit status: $status"
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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26 # Check for successful completion
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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27 if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ] ; then
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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28 echo "Trimmomatic did not finish successfully" >&2
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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29 exit 1
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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30 fi
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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31 exit $status
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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32 ##
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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33 #