Mercurial > repos > iuc > package_r_3_2_1

annotate tool_dependencies.xml @ 2:2ce7fd67f394 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
author iuc
date Thu, 03 Dec 2015 07:23:45 -0500
parents fae49a02a848
children d0bf97420fb5
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e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
iuc
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diff changeset
1 <?xml version="1.0"?>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
iuc
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2 <tool_dependency>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
iuc
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3 <package name="R" version="3.2.1">
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
iuc
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4 <install version="1.0">
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
iuc
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5 <actions_group>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
iuc
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6 <actions architecture="x86_64" os="linux">
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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7 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tar.gz</action>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
iuc
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8 <action type="move_directory_files">
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
iuc
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9 <source_directory>.</source_directory>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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10 <destination_directory>$INSTALL_DIR</destination_directory>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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11 </action>
2
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
iuc
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12 <action type="shell_command">
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
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13 command -v gfortran || return 0
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
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14 BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 &amp;&amp;
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
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15 BUNDLED_LGF_FQSO=$INSTALL_DIR/lib/libgfortran.so.3 &amp;&amp;
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
iuc
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16 BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &amp;&amp;
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
iuc
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17 echo 'program test; end program test' &gt; test.f90 &amp;&amp;
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
iuc
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18 gfortran -o test test.f90 &amp;&amp;
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
iuc
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19 LGF=`ldd test | grep libgfortran | awk '{print $3}'` &amp;&amp;
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
iuc
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20 LGF_CANON=`readlink -f $LGF` &amp;&amp;
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
iuc
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21 LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &amp;&amp;
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
iuc
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22 if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
iuc
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23 cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled &amp;&amp;
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
iuc
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24 cp -p $BUNDLED_LGF_FQSO ${BUNDLED_LGF_FQSO}.bundled &amp;&amp;
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
iuc
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25 cp -p $LGF_CANON $BUNDLED_LGF_CANON &amp;&amp;
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
iuc
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26 cp -p $LGF_CANON $BUNDLED_LGF_FQSO
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
iuc
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27 fi
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
iuc
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28 </action>
0
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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29 <action type="set_environment">
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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30 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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31 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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32 </action>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
iuc
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33 </actions>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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34 <actions>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
iuc
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35 <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.2.1.tar.gz</action>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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36 <package name="atlas" version="3.10.2">
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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37 <repository changeset_revision="0538fd672119" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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38 </package>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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39 <package name="readline" version="6.3">
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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40 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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41 </package>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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42 <package name="libpng" version="1.6.7">
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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43 <repository changeset_revision="05df724aefbb" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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44 </package>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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45 <package name="cairo" version="1.12.14">
2
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46 <repository changeset_revision="3d4edf152b1b" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
0
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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47 </package>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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48 <package name="pixman" version="0.32.6">
2
2ce7fd67f394 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
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49 <repository changeset_revision="06f701aa92e2" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
0
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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50 </package>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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51 <package name="freetype" version="2.5.2">
2
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52 <repository changeset_revision="3b09e7916896" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
0
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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53 </package>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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54 <package name="ncurses" version="6.0">
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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55 <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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56 </package>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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57 <package name="fontconfig" version="2.11.1">
2
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58 <repository changeset_revision="2ce32675340e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
0
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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59 </package>
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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60 <action type="set_environment_for_install">
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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61 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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62 <package name="readline" version="6.3" />
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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63 </repository>
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64 <repository changeset_revision="05df724aefbb" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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65 <package name="libpng" version="1.6.7" />
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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66 </repository>
2
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67 <repository changeset_revision="3d4edf152b1b" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
0
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68 <package name="cairo" version="1.12.14" />
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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69 </repository>
2
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70 <repository changeset_revision="06f701aa92e2" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
0
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71 <package name="pixman" version="0.32.6" />
e46a7803f17b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
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72 </repository>
2
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73 <repository changeset_revision="3b09e7916896" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
0
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74 <package name="freetype" version="2.5.2" />
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75 </repository>
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76 <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
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77 <package name="ncurses" version="6.0" />
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78 </repository>
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79 <repository changeset_revision="2ce32675340e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
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80 <package name="fontconfig" version="2.11.1" />
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81 </repository>
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82 </action>
2
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83 <action type="autoconf">--with-tcltk --with-blas --with-lapack --with-readline --with-cairo --with-libpng --without-x --enable-R-shlib --disable-R-framework --libdir=$INSTALL_DIR/lib</action>
0
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84 <action type="make_install" />
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85 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
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86 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
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87 </actions>
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88 <action type="set_environment">
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89 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
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90 <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable>
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91 <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable>
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92 <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable>
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93 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
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94 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
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95 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
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96 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
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97 <environment_variable action="prepend_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
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98 <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
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99 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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100 </action>
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101 </actions_group>
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102 </install>
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103 <readme>
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104 The precompiled versions of this package were built 2015-07-27.
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105 R is a free software environment for statistical computing and graphics.
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106 NOTE: See custom compilation options above.
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107 </readme>
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108 </package>
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109 </tool_dependency>