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35
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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36
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3 <package name="R_3_0_1" version="3.0.1">
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4 <repository changeset_revision="4e9dce1105cd" name="precommit_test" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6
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7
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8
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9 <package name="deseq2" version="1.0.17">
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35
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10 <install version="1.0">
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11 <actions>
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36
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12 <action type="download_file">http://bioconductor.org/packages/release/bioc/src/contrib/DESeq2_1.0.17.tar.gz</action>
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13
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14 <action type="set_environment_for_install">
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15 <repository changeset_revision="4e9dce1105cd" name="precommit_test" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
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16 <package name="R_3_0_1" version="3.0.1" />
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17 </repository>
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18 </action>
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19
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20 <action type="make_directory">$INSTALL_DIR/deseq2/</action>
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21 <action type="shell_command">
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22 Rscript -e "source('http://bioconductor.org/biocLite.R'); install.packages('DESeq2', lib='$INSTALL_DIR/deseq2/', repos='http://cran.us.r-project.org')"
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23 </action>
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35
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24 <action type="set_environment">
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36
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25 <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/deseq2/</environment_variable>
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35
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26 </action>
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27 </actions>
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28 </install>
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36
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29 <readme>DESeq2</readme>
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35
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30 </package>
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31 </tool_dependency>
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