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annotate tool_dependencies.xml @ 0:acb56603b268 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
author yhoogstrate
date Mon, 31 Aug 2015 11:00:02 -0400
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children a4a4c88783ea
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acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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1 <?xml version="1.0"?>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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2 <tool_dependency>
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3 <package name="R" version="3.0.3">
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4 <repository changeset_revision="a8438aa1207c" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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5 </package>
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acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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7 <package name="biocLite_edgeR_limma" version="latest">
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8 <install version="1.0">
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9 <actions>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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10 <action type="set_environment_for_install">
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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11 <repository changeset_revision="a8438aa1207c" name="package_r_3_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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12 <package name="R" version="3.0.3" />
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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13 </repository>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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15 </action>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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16 <action type="make_directory">$INSTALL_DIR</action>
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17 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &gt; $INSTALL_DIR/runme.R</action>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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18 <action type="shell_command">echo "installme=c('edgeR','limma')" &gt;&gt; $INSTALL_DIR/runme.R</action>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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19 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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20 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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21 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" &gt;&gt; $INSTALL_DIR/runme.R</action>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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22 <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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23 <action type="shell_command">export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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24 </actions>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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25 </install>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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26 <readme>
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27 Installs the latest bioc packages: edgeR &amp; Limma
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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28 </readme>
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29 </package>
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30
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31 <package name="design_matrix_creator" version="1.0.0">
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32 <install version="1.0">
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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33 <actions>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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34 <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/design_matrix_creator $INSTALL_DIR/bin/</action>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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35 <action type="chmod">
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36 <file mode="755">$INSTALL_DIR/bin/design_matrix_creator</file>
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37 </action>
acb56603b268 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 65724bff3df1267a185b54c1646c96a200528eae
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38 <action type="set_environment">
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39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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40 <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
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41 </action>
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42 </actions>
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43 </install>
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44 </package>
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45
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46 <package name="edger_dge_table_to_bedgraph" version="1.0.0">
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47 <install version="1.0">
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48 <actions>
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49 <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/edger_dge_table_to_bedgraph $INSTALL_DIR/bin/</action>
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50 <action type="chmod">
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51 <file mode="755">$INSTALL_DIR/bin/edger_dge_table_to_bedgraph</file>
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52 </action>
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53 <action type="set_environment">
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54 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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55 <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
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56 </action>
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57 </actions>
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58 </install>
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59 </package>
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60 </tool_dependency>