Mercurial > repos > eganrol > rnaseqdataannotation

comparison RNAseqDataAnnotation/tool_dependencies.xml @ 18:d1a60d1848d9 draft

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author eganrol
date Thu, 20 Nov 2014 03:51:36 -0500
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17:1a717a89610a 18:d1a60d1848d9
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="R_3_0_2" version="3.0.2">
4 <repository changeset_revision="b6fe8ca3230d" name="package_r_3_0_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="DESeq2biomaRt" version="1.0">
7 <install version="1.0">
8 <actions>
9 <action type="set_environment_for_install">
10 <repository changeset_revision="b6fe8ca3230d" name="package_r_3_0_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
11 <package name="R_3_0_2" version="3.0.2" />
12 </repository>
13 </action>
14 <action type="shell_command">R CMD BATCH source("http://bioconductor.org/biocLite.R")</action>
15 <action type="shell_command">R CMD BATCH biocLite()</action>
16 <action type="shell_command">R CMD BATCH biocLite("DESeq2")</action>
17 <action type="shell_command">R CMD BATCH biocLite("biomaRt")</action>
18 <action type="shell_command">R CMD BATCH install.packages("plyr")</action>
19 <!--<action type="shell_command">echo "export PATH=$PATH" > $INSTALL_DIR/env.sh </action>-->
20 <!--<action type="shell_command">chmod 755 $INSTALL_DIR/env.sh </action>-->
21 </actions>
22 </install>
23 <readme>
24 </readme>
25 </package>
26 </tool_dependency>