Mercurial > repos > iuc > package_r_3_0_1_with_atlas
annotate tool_dependencies.xml @ 0:4aa16d4746cb draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
author | iuc |
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date | Tue, 19 May 2015 15:01:02 -0400 |
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4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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1 <?xml version="1.0"?> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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2 <tool_dependency> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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3 <package name="atlas" version="3.10.1"> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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4 <repository changeset_revision="37ff27ea37ed" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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5 </package> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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6 <package name="readline" version="6.2"> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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7 <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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8 </package> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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9 <package name="R_3_0_1" version="3.0.1"> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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10 <install version="1.0"> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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11 <actions> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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12 <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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13 <action type="set_environment_for_install"> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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14 <repository changeset_revision="37ff27ea37ed" name="package_atlas_3_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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15 <package name="atlas" version="3.10.1" /> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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16 </repository> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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17 <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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18 <package name="readline" version="6.2" /> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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19 </repository> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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20 </action> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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21 |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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22 <action language="cheetah" type="template_command"> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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23 #set $cmd = './configure' |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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24 #if env.get('ATLAS_LIB_DIR', False): |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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25 #set $cmd += ' --with-blas="-L%s -lptf77blas -lpthread -latlas" ' % $env.ATLAS_LIB_DIR |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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26 #end if |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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27 |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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28 #if env.get('READLINE_LIB_PATH', False): |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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29 export LDFLAGS=-L$env.READLINE_LIB_PATH && |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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30 export CPPFLAGS=-I$env.READLINE_INCLUDE_PATH && |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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31 #set $cmd += ' --with-readline=yes ' |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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32 #else: |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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33 #set $cmd += ' --with-readline=no ' |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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34 #end if |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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35 |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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36 #set $cmd += ' --enable-R-shlib --with-x=no --libdir=%s/lib/ --bindir=%s/bin/ --datarootdir=%s/share/' % ($env.INSTALL_DIR, $env.INSTALL_DIR, $env.INSTALL_DIR) |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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37 $cmd |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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38 </action> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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39 <action type="shell_command">make</action> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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40 <action type="shell_command">make install</action> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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41 <action type="set_environment"> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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42 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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43 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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44 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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45 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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46 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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47 <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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48 </action> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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49 </actions> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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50 </install> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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51 <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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52 </package> |
4aa16d4746cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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53 </tool_dependency> |