Mercurial > repos > iuc > package_r_3_1_2

comparison tool_dependencies.xml @ 4:4d2fd1413b56 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_2 commit 9a9d44116b21d9a155b5cc274475e78c14915059
author iuc
date Thu, 07 Apr 2016 11:23:03 -0400
parents c987143177d4
children
comparison
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3:c987143177d4 4:4d2fd1413b56
2 <tool_dependency> 2 <tool_dependency>
3 <package name="R" version="3.1.2"> 3 <package name="R" version="3.1.2">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions_group> 5 <actions_group>
6 <actions architecture="x86_64" os="linux"> 6 <actions architecture="x86_64" os="linux">
7 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.1.2-Linux-x84_64.tgz</action> 7 <action sha256sum="586dde39d6821bcc5079004450f5d19f836a26d4554083c7add3933f071451e0" type="download_by_url">https://depot.galaxyproject.org/software/r/r_3.1.2_linux_x64.tar.gz</action>
8 <action type="move_directory_files"> 8 <action type="move_directory_files">
9 <source_directory>.</source_directory> 9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR</destination_directory> 10 <destination_directory>$INSTALL_DIR</destination_directory>
11 </action> 11 </action>
12 <action type="set_environment"> 12 <action type="set_environment">
13 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable> 13 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
14 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable> 14 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
15 </action> 15 </action>
16 </actions> 16 </actions>
17 <actions architecture="x86_64" os="darwin"> 17 <actions>
18 <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.1.2.tar.gz</action> 18 <action sha256sum="bcd150afcae0e02f6efb5f35a6ab72432be82e849ec52ce0bb89d8c342a8fa7a" type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.1.2.tar.gz</action>
19 <package name="readline" version="6.2"> 19 <package name="readline" version="6.2">
20 <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 20 <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
21 </package> 21 </package>
22 <package name="libpng" version="1.6.7"> 22 <package name="libpng" version="1.6.7">
23 <repository changeset_revision="f48b920cae1f" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 23 <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
24 </package> 24 </package>
25 <package name="cairo" version="1.12.14"> 25 <package name="cairo" version="1.12.14">
26 <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 26 <repository changeset_revision="cd2ed5717e38" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
27 </package> 27 </package>
28 <package name="pixman" version="0.32.4"> 28 <package name="pixman" version="0.32.4">
29 <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 29 <repository changeset_revision="93cd8e03820c" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
30 </package> 30 </package>
31 <package name="freetype" version="2.5.2"> 31 <package name="freetype" version="2.5.2">
32 <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 32 <repository changeset_revision="a65217367e4a" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
33 </package> 33 </package>
34 <package name="ncurses" version="5.9"> 34 <package name="ncurses" version="5.9">
35 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 35 <repository changeset_revision="a6cbb3aaecf6" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
36 </package>
37 <package name="fontconfig" version="2.11.1">
38 <repository changeset_revision="466900d2014a" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
36 </package> 39 </package>
37 <action type="set_environment_for_install"> 40 <action type="set_environment_for_install">
38 <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> 41 <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
39 <package name="readline" version="6.2" /> 42 <package name="readline" version="6.2" />
40 </repository> 43 </repository>
41 <repository changeset_revision="f48b920cae1f" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> 44 <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
42 <package name="libpng" version="1.6.7" /> 45 <package name="libpng" version="1.6.7" />
43 </repository> 46 </repository>
44 <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> 47 <repository changeset_revision="cd2ed5717e38" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
45 <package name="cairo" version="1.12.14" /> 48 <package name="cairo" version="1.12.14" />
46 </repository> 49 </repository>
47 <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> 50 <repository changeset_revision="93cd8e03820c" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
48 <package name="pixman" version="0.32.4" /> 51 <package name="pixman" version="0.32.4" />
49 </repository> 52 </repository>
50 <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> 53 <repository changeset_revision="a65217367e4a" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
51 <package name="freetype" version="2.5.2" /> 54 <package name="freetype" version="2.5.2" />
52 </repository> 55 </repository>
53 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> 56 <repository changeset_revision="a6cbb3aaecf6" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
54 <package name="ncurses" version="5.9" /> 57 <package name="ncurses" version="5.9" />
55 </repository> 58 </repository>
59 <repository changeset_revision="466900d2014a" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
60 <package name="fontconfig" version="2.11.1" />
61 </repository>
56 </action> 62 </action>
57 <action type="shell_command"> 63 <action type="autoconf">--with-tcltk --with-blas --with-lapack --with-readline --with-cairo --with-libpng --without-x --without-aqua --enable-R-shlib --disable-R-framework --libdir=$INSTALL_DIR/lib</action>
58 export LDFLAGS="-L$PNG_LIBS -L$NCURSES_LIB_PATH -L$READLINE_LIB_PATH" &amp;&amp;
59 export LDFLAGS="$LDFLAGS -Wl,-rpath,$NCURSES_LIB_PATH" &amp;&amp;
60 export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &amp;&amp;
61 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &amp;&amp;
62 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" &amp;&amp;
63 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
64 export CFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" &amp;&amp;
65 export CXXFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" &amp;&amp;
66 export CPPFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" &amp;&amp;
67 ./configure --with-tcltk \
68 --with-blas \
69 --with-lapack \
70 --with-readline \
71 --with-cairo \
72 --with-libpng \
73 --without-x \
74 --enable-R-shlib \
75 --disable-R-framework \
76 --libdir=$INSTALL_DIR/lib \
77 --prefix=$INSTALL_DIR
78 </action>
79 <action type="make_install" />
80 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action> 64 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
81 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action> 65 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
82 </actions> 66 </actions>
83 <action type="set_environment"> 67 <action type="set_environment">
84 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable> 68 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>