Mercurial > repos > sanbi-uwc > trimmomatic

annotate package_trimmomatic.sh @ 1:bbe75c52b300 draft

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planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 0c8f6d302eafe1ee9fb8a2adac3fe37a8082628d
author sanbi-uwc
date Fri, 20 Jan 2017 08:57:21 -0500
parents d8975856862e
children 642a39a927c9
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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
parents:
diff changeset
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 # Package Trimmomatic tool files into tgz file for upload to
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 # Galaxy toolshed
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 #
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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6 TGZ=trimmomatic.tgz
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
diff changeset
7 if [ -f $TGZ ] ; then
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
diff changeset
8 echo $TGZ: already exists, please remove >&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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9 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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10 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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11 tar cvzf $TGZ \
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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12 README.rst \
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 trimmomatic.xml \
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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14 trimmomatic.sh \
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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15 tool_dependencies.xml \
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 test-data
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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17 if [ -f $TGZ ] ; 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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18 echo Created $TGZ
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 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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20 echo Failed to created $TGZ >&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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21 exit 1
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 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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23 ##
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 #