Mercurial > repos > sanbi-uwc > trimmomatic

annotate trimmomatic_BASE_16925.sh @ 4:642a39a927c9 draft

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planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
author sanbi-uwc
date Mon, 23 Jan 2017 07:46:47 -0500
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642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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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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diff changeset
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
parents:
diff changeset
4 echo Arguments:
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
parents:
diff changeset
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
parents:
diff changeset
6 echo "*" $i
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
parents:
diff changeset
7 done
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
parents:
diff changeset
8 java $@ 2>&1 | tee trimmomatic.log
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
parents:
diff changeset
9 status=$?
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
parents:
diff changeset
10 echo "Exit status: $status"
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
parents:
diff changeset
11 # Check for successful completion
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
parents:
diff changeset
12 if [ -z "$(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
parents:
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13 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
sanbi-uwc
parents:
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14 exit 1
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
parents:
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15 fi
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
parents:
diff changeset
16 exit $status
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
parents:
diff changeset
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 #