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1 <?xml version="1.0"?>
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2 <tool_dependency>
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1
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3
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4 <!-- R -->
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5 <package name="R" version="3.1.2">
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6 <repository changeset_revision="d2f70822dc31" name="package_r_3_1_2_rjava" owner="morinlab" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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7 </package>
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8
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9 <!-- Morinlab scripts with EXPANDS wrapper script -->
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10 <package name="morinlab_scripts" version="14.2">
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11 <repository changeset_revision="b88b230de028" name="package_morinlab_scripts_14_2" owner="morinlab" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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12 </package>
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13
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14 <!-- EXPANDS and other R packages -->
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15 <package name="expands" version="1.7.2">
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16
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17 <install version="1.0">
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18 <actions>
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19
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20 <action type="set_environment_for_install">
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21 <repository changeset_revision="d2f70822dc31" name="package_r_3_1_2_rjava" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu">
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22 <package name="R" version="3.1.2" />
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23 </repository>
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24 </action>
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25
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26 <action type="shell_command">R CMD javareconf -e</action>
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27
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28 <action type="setup_r_environment">
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29 <repository changeset_revision="d2f70822dc31" name="package_r_3_1_2_rjava" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu">
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30 <package name="R" version="3.1.2" />
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31 </repository>
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32 <package>https://cran.r-project.org/src/contrib/modeltools_0.2-21.tar.gz</package>
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33 <package>https://cran.r-project.org/src/contrib/mclust_5.2.tar.gz</package>
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34 <package>https://cran.r-project.org/src/contrib/Archive/nnet/nnet_7.3-11.tar.gz</package>
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35 <package>https://cran.r-project.org/src/contrib/flexmix_2.3-13.tar.gz</package>
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36 <package>https://cran.r-project.org/src/contrib/Archive/nlme/nlme_3.1-122.tar.gz</package>
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37 <package>https://cran.r-project.org/src/contrib/ape_3.5.tar.gz</package>
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38 <package>https://cran.r-project.org/src/contrib/permute_0.9-0.tar.gz</package>
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39 <package>https://cran.r-project.org/src/contrib/moments_0.14.tar.gz</package>
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40 <package>https://cran.r-project.org/src/contrib/lattice_0.20-33.tar.gz</package>
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41 <package>https://cran.r-project.org/src/contrib/argparser_0.4.tar.gz</package>
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42 <package>https://cran.r-project.org/src/contrib/matlab_1.0.2.tar.gz</package>
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43 <package>https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz</package>
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44 <package>https://cran.r-project.org/src/contrib/Archive/digest/digest_0.6.9.tar.gz</package>
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45 <package>https://cran.r-project.org/src/contrib/gtable_0.2.0.tar.gz</package>
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46 <package>https://cran.r-project.org/src/contrib/Archive/Rcpp/Rcpp_0.12.5.tar.gz</package>
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47 <package>https://cran.r-project.org/src/contrib/Archive/plyr/plyr_1.8.3.tar.gz</package>
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48 <package>https://cran.r-project.org/src/contrib/Archive/stringi/stringi_1.0-1.tar.gz</package>
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49 <package>https://cran.r-project.org/src/contrib/Archive/stringr/stringr_0.6.2.tar.gz</package>
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50 <package>https://cran.r-project.org/src/contrib/Archive/reshape2/reshape2_1.4.tar.gz</package>
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51 <package>https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz</package>
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52 <package>https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz</package>
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53 <package>https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz</package>
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54 <package>https://cran.r-project.org/src/contrib/Archive/munsell/munsell_0.4.tar.gz</package>
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55 <package>https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz</package>
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56 <package>https://cran.r-project.org/src/contrib/Archive/scales/scales_0.3.0.tar.gz</package>
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57 <package>https://cran.r-project.org/src/contrib/ggplot2_2.1.0.tar.gz</package>
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58 <package>https://cran.r-project.org/src/contrib/ggrepel_0.5.tar.gz</package>
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59 <package>https://cran.r-project.org/src/contrib/assertthat_0.1.tar.gz</package>
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60 <package>https://cran.r-project.org/src/contrib/lazyeval_0.2.0.tar.gz</package>
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61 <package>https://cran.r-project.org/src/contrib/tibble_1.1.tar.gz</package>
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62 <package>https://cran.r-project.org/src/contrib/Archive/DBI/DBI_0.4-1.tar.gz</package>
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63 <package>https://cran.r-project.org/src/contrib/Archive/R6/R6_2.1.1.tar.gz</package>
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64 <package>https://cran.r-project.org/src/contrib/Archive/BH/BH_1.60.0-1.tar.gz</package>
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65 <package>https://cran.r-project.org/src/contrib/dplyr_0.5.0.tar.gz</package>
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66 <package>https://cran.r-project.org/src/contrib/expands_1.7.2.tar.gz</package>
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67 </action>
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68 </actions>
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69
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70 </install>
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71
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72 </package>
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73 <readme>
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74 Expanding Ploidy and Allele Frequency on Nested Subpopulations (EXPANDS) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome-sequencing input data.
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75 </readme>
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76 </tool_dependency>
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