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24
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3
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63
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4 <!-- the following repo does NOT work out of the box:
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58
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5 <package name="package_r3_withx" version="3.0.1">
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6 <repository changeset_revision="abc274f22004" name="package_r3_withx" owner="joachim-jacob" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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24
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7 </package>
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63
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8 -->
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64
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9
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66
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10 <!-- the following repo does NOT even install due to gfortran shared libs:
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64
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11 <package name="R" version="3.1.0">
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12 <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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63
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13 </package>
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66
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14 -->
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15
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16 <package name="R" version="3.0.3">
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68
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17 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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66
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18 </package>
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24
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19
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78
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20 <package name="biocLite_edgeR_limma" version="latest">
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24
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21 <install version="1.0">
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22 <actions>
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23 <action type="set_environment_for_install">
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61
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24 <!-- the following repo does NOT work out of the box:
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56
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25 <repository changeset_revision="abc274f22004" name="package_r3_withx" owner="joachim-jacob" toolshed="http://testtoolshed.g2.bx.psu.edu/">
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26 <package name="package_r3_withx" version="3.0.1" />
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27 </repository>
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61
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28 -->
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66
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29 <!-- the following repo does NOT even install due to gfortran shared libs:
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64
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30 <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
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31 <package name="R" version="3.1.0" />
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61
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32 </repository>
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66
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33 -->
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34
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68
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35 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
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66
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36 <package name="R" version="3.0.3" />
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37 </repository>
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38
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24
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39 </action>
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40 <action type="make_directory">$INSTALL_DIR</action>
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41 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action>
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42 <action type="shell_command">echo "installme=c('edgeR','limma')" >> $INSTALL_DIR/runme.R</action>
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43 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action>
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44 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action>
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45 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" >> $INSTALL_DIR/runme.R</action>
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46 <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action>
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47 <action type="shell_command">export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action>
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48 </actions>
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49 </install>
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50 <readme>
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66
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51 Installs the latest bioc packages: edgeR & Limma
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24
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52 </readme>
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53 </package>
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54
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71
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55 <!-- instead of using "convert", make use of "gm convert" -->
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56 <package name="graphicsmagick" version="1.3.18">
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74
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57 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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71
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58 </package>
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24
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59 </tool_dependency>
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