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planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
author yating-l
date Wed, 21 Dec 2016 12:13:04 -0500
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f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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1 #!/usr/bin/env bash
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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3 localBinPath="/usr/local/bin/"
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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4 hgDownloadURl="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/"
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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6 # Binaries needed for HAC
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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7 twoBitInfo="twoBitInfo"
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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8 faToTwoBit="faToTwoBit"
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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9 gff3ToGenePred="gff3ToGenePred"
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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10 gtfToGenePred="gtfToGenePred"
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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11 genePredToBed="genePredToBed"
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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12 # sort="sort"
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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13 bedToBigBed="bedToBigBed"
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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15 binariesArray=( ${twoBitInfo} ${faToTwoBit} ${gff3ToGenePred} ${gtfToGenePred} ${genePredToBed} ${bedToBigBed} )
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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17 # Download and install binaries
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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18 for binaryName in "${binariesArray[@]}"
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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19 do
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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20 binaryInstallationPath="${localBinPath}/${binaryName}"
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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21 sudo wget -P ${localBinPath} "${hgDownloadURl}/${binaryName}"
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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22 sudo chown ${USER} ${binaryInstallationPath}
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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23 sudo chmod +x ${binaryInstallationPath}
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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24 done