|
24
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
|
3
|
|
33
|
4 <package name="R" version="3.0.3">
|
|
28
|
5 <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
|
|
24
|
6 </package>
|
|
|
7
|
|
28
|
8 <package name="package_biocLite_edgeR_limma" version="latest">
|
|
24
|
9 <install version="1.0">
|
|
|
10 <actions>
|
|
|
11 <action type="set_environment_for_install">
|
|
28
|
12 <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
|
|
|
13 <package name="package_r_3_0_3" version="3.0.3" />
|
|
24
|
14 </repository>
|
|
|
15 </action>
|
|
|
16 <action type="make_directory">$INSTALL_DIR</action>
|
|
|
17 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action>
|
|
|
18 <action type="shell_command">echo "installme=c('edgeR','limma')" >> $INSTALL_DIR/runme.R</action>
|
|
|
19 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action>
|
|
|
20 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action>
|
|
|
21 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" >> $INSTALL_DIR/runme.R</action>
|
|
|
22 <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action>
|
|
|
23 <action type="shell_command">export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action>
|
|
|
24 </actions>
|
|
|
25 </install>
|
|
|
26 <readme>
|
|
28
|
27 Installs the latest bioc packages edgeR & Limma
|
|
24
|
28 </readme>
|
|
|
29 </package>
|
|
|
30
|
|
|
31 </tool_dependency>
|
