Mercurial > repos > sanbi-uwc > trimmomatic

annotate install_tool_deps.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
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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/bash
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 # Install dependencies for Trimmomatic for testing from the command line
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 #
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 # Installer functions
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 . $(dirname $0)/../../local_dependency_installers/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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7 # Installation directory
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 TOP_DIR=$1
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
diff changeset
9 if [ -z "$TOP_DIR" ] ; 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 echo Usage: $(basename $0) DIR
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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11 exit
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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12 fi
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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13 if [ -z "$(echo $TOP_DIR | grep ^/)" ] ; then
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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14 TOP_DIR=$(pwd)/$TOP_DIR
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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15 fi
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
parents:
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16 if [ ! -d "$TOP_DIR" ] ; 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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17 mkdir -p $TOP_DIR
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 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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19 # Trimmomatic 0.32
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
sanbi-uwc
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20 install_trimmomatic_0_36 $TOP_DIR
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 ##
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 #