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2
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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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4 <package name="R" version="3.1.2">
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5
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6 <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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7
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8 </package>
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9
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10
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11 <package name="mpagenomics" version="1.1.2">
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12
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13 <install version="1.0">
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14
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15 <actions>
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16
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17 <action type="set_environment_for_install">
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18
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19 <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" toolshed="http://localhost:9009">
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20
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21 <package name="R" version="3.1.2" />
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22
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23 </repository>
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24
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25 </action>
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26
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27
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28 <!--action type="download_file">http://www.bioconductor.org/packages/release/bioc/src/contrib/DNAcopy_1.42.0.tar.gz</action>
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29 <action type="download_file">http://cran.r-project.org/src/contrib/MPAgenomics_1.1.2.tar.gz</action>
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30 <action type="download_file">http://www.braju.com/R/repos/sfit_0.3.0.tar.gz</action>
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31 <action type="download_file">http://www.bioconductor.org/packages/release/bioc/src/contrib/affxparser_1.40.0.tar.gz</action>
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32
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33 <action type="download_file">http://www.bioconductor.org/packages/release/bioc/src/contrib/aroma.light_2.4.0.tar.gz</action>
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34
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35 <action type="download_file">http://cran.r-project.org/src/contrib/aroma.affymetrix_2.13.0.tar.gz</action>
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36 <action type="download_file">http://cran.r-project.org/src/contrib/aroma.cn_1.6.0.tar.gz</action-->
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37 <action type="make_directory">$INSTALL_DIR/mpagenomics/</action>
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38
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39 <action type="shell_command">
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40
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41 export PATH=$PATH:$R_HOME/bin &&
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42
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43 export R_LIBS=$INSTALL_DIR/mpagenomics/ &&
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44
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45 Rscript -e "source('http://www.braju.com/R/hbLite.R')" -e "hbLite('sfit')" -e "source('http://bioconductor.org/biocLite.R')" -e "biocLite('affxparser')" -e "biocLite('DNAcopy')" -e "biocLite('aroma.light')" -e "install.packages(c('aroma.affymetrix','aroma.cn'),lib='$INSTALL_DIR/mpagenomics/', repos='http://cran.us.r-project.org', dependencies=TRUE)" -e "install.packages('MPAgenomics',lib='$INSTALL_DIR/mpagenomics/', repos='http://cran.us.r-project.org', dependencies=TRUE)"
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46 </action>
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47 <action type="set_environment">
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48
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49 <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/mpagenomics/</environment_variable>
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50
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51 </action>
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52
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53 </actions>
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54
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55 </install>
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56
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57 <readme>
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58
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59 mpagenomics
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60
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61 Ubuntu has a bug with libgfortran. To fix that create a symlink like: sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/x86_64-linux-gnu/libgfortran.so
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62
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63 </readme>
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64
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65 </package>
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66
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67 </tool_dependency>
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