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20
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="R_3_0_2" version="3.0.2">
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4 <repository changeset_revision="b6fe8ca3230d" name="package_r_3_0_2" owner="iuc" prior_installation_required="True" toolshed="testtoolshed.g2.bx.psu.edu"/>
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5 </package>
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6 <package name="DESeq2biomaRt" version="1.0">
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7 <install version="1.0">
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8 <actions>
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9 <action type="set_environment_for_install">
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10 <repository changeset_revision="b6fe8ca3230d" name="package_r_3_0_2" owner="iuc" prior_installation_required="True" toolshed="testtoolshed.g2.bx.psu.edu">
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11 <package name="R_3_0_2" version="3.0.2"/>
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12 </repository>
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13 </action>
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14 <action type="shell_command">R CMD BATCH source("http://bioconductor.org/biocLite.R")</action>
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15 <action type="shell_command">R CMD BATCH biocLite()</action>
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16 <action type="shell_command">R CMD BATCH biocLite("DESeq2")</action>
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17 <action type="shell_command">R CMD BATCH biocLite("biomaRt")</action>
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18 <action type="shell_command">R CMD BATCH install.packages("plyr")</action>
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19 <!--<action type="shell_command">echo "export PATH=$PATH" > $INSTALL_DIR/env.sh </action>-->
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20 <!--<action type="shell_command">chmod 755 $INSTALL_DIR/env.sh </action>-->
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21 </actions>
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22 </install>
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23 <readme>
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24 </readme>
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25 </package>
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26 </tool_dependency>
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