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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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3
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12
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4 <!--
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5 <package name="R" version="3.1.0">
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12
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6 <repository name="package_r_3_1_0" owner="iuc" prior_installation_required="True" />
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3
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7 </package>
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12
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8 -->
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14
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9 <package name="R_3_1_1 " version="3.1.1">
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10 <repository changeset_revision="d9964efbfbe3" name="package_r_3_1_1" owner="fubar" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12
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17
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13 <package name="qdnaseq" version="1.0.5">
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3
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14 <install version="1.0">
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15 <actions>
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12
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16 <action type="shell_command">echo "[DEBUG] Starting install actions"</action>
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3
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17 <action type="setup_r_environment">
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18
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18
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19 <!-- originally tried 3_1_0 but multiple errors -->
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12
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20 <!--
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21 <repository name="package_r_3_1_0" owner="iuc">
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3
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22 <package name="R" version="3.1.0" />
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23 </repository>
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10
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24 -->
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25
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18
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26 <!-- this one has to compile but works in all tests I did -->
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27 <repository changeset_revision="d9964efbfbe3" name="package_r_3_1_1" owner="fubar" toolshed="https://testtoolshed.g2.bx.psu.edu">
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28 <package name="R_3_1_1" version="3.1.1" />
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12
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29 </repository>
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30
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9
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31 <!--
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32 <action type="shell_command">Rscript -e "source(\"http://bioconductor.org/biocLite.R\"); biocLite(); biocLite(\"QDNAseq\"")"</action>
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9
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33 -->
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12
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34
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35 <!-- HERE all the packages hosted at bitbucket -->
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36 <!-- currently breaks at DNAcopy with R3.1.0 iuc dep pack -->
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37 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.methodsS3_1.6.1.tar.gz</package>
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38 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/matrixStats_0.10.0.tar.gz</package>
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39 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.oo_1.18.0.tar.gz</package>
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40 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.utils_1.32.4.tar.gz</package>
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41 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/BiocGenerics_0.10.0.tar.gz</package>
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42 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Biobase_2.24.0.tar.gz</package>
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43 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/limma_3.20.5.tar.gz</package>
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44 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/marray_1.42.0.tar.gz</package>
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45 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/CGHbase_1.24.0.tar.gz</package>
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46 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/impute_1.38.1.tar.gz</package>
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13
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47 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/DNAcopy_1.38.1.tar.gz</package>
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10
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48 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/snow_0.3-13.tar.gz</package>
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49 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/snowfall_1.84-6.tar.gz</package>
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50 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/CGHcall_2.26.0.tar.gz</package>
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51 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/IRanges_1.22.9.tar.gz</package>
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52 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/GenomeInfoDb_1.0.2.tar.gz</package>
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53 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/XVector_0.4.0.tar.gz</package>
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54 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/GenomicRanges_1.16.4.tar.gz</package>
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55 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/zlibbioc_1.10.0.tar.gz</package>
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56 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Biostrings_2.32.1.tar.gz</package>
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57 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/bitops_1.0-6.tar.gz</package>
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58 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Rsamtools_1.16.1.tar.gz</package>
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59 <package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/QDNAseq_1.0.5.tar.gz</package>
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60
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3
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61 </action>
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62 <action type="shell_command">echo "[DEBUG] ...done with install actions"</action>
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3
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63 </actions>
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64 </install>
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65 <readme>
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66 Prepares R Bioconductor package "QDNAseq" and all of its dependencies.
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67 </readme>
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68 </package>
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69 </tool_dependency>
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