Mercurial > repos > yating-l > hubarchivecreator
annotate util/install_linux_binaries @ 0:f493979f1408 draft default tip
planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
author | yating-l |
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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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2 |
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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5 |
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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diff
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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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14 |
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} ${bedToBigBed} ) |
f493979f1408
planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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16 |
f493979f1408
planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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17 # Download and install binaries |
f493979f1408
planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
yating-l
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18 for binaryName in "${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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diff
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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 |