Mercurial > repos > sanbi-uwc > trimmomatic

annotate trimmomatic.sh @ 3:f6cb99d6afd3 draft

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planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 213668d2e5a61c806ad992c201ae6e304c6e0965-dirty
author sanbi-uwc
date Mon, 23 Jan 2017 06:31:29 -0500
parents d8975856862e
children
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d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
diff changeset
1 #!/bin/sh
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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2 #
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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3 # Shell wrapper to run Trimmomatic jar file as a Galaxy tool
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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4 echo Arguments:
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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5 for i in $@ ; do
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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6 echo "*" $i
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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7 done
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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8
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
diff changeset
9 if [ -n "$CONDA_PREFIX" ] ; then
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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10 # bioconda installs trimmomatic in a share directory
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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11 # with a jarfile called trimmomatic.jar
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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12 TRIMMOMATIC_DIR="$CONDA_PREFIX/share/trimmomatic"
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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13 JARFILE="trimmomatic.jar"
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
diff changeset
14 else
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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15 JARFILE="trimmomatic-0.36.jar"
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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16 fi
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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17
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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18 if [ -z "$TRIMMOMATIC_DIR" ] ; then
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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19 echo "TRIMMOMATIC_DIR variable not set, can't find jar file"
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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20 exit 1
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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21 fi
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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22
3
f6cb99d6afd3 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 213668d2e5a61c806ad992c201ae6e304c6e0965-dirty
sanbi-uwc
parents: 0
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23 java -mx16G -jar $TRIMMOMATIC_DIR/$JARFILE $@ 2>&1 | tee trimmomatic.log
0
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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24 status=$?
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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25 echo "Exit status: $status"
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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26 # Check for successful completion
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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27 if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ] ; then
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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28 echo "Trimmomatic did not finish successfully" >&2
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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29 exit 1
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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30 fi
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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31 exit $status
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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32 ##
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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33 #