Mercurial > repos > iuc > package_r_3_2_1

comparison 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
comparison
equal deleted inserted replaced
1:fae49a02a848 2:2ce7fd67f394
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-3.2.1-Linux-x86_64.tar.gz</action> 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>
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>
12 <action type="shell_command">
13 command -v gfortran || return 0
14 BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 &amp;&amp;
15 BUNDLED_LGF_FQSO=$INSTALL_DIR/lib/libgfortran.so.3 &amp;&amp;
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;
17 echo 'program test; end program test' &gt; test.f90 &amp;&amp;
18 gfortran -o test test.f90 &amp;&amp;
19 LGF=`ldd test | grep libgfortran | awk '{print $3}'` &amp;&amp;
20 LGF_CANON=`readlink -f $LGF` &amp;&amp;
21 LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &amp;&amp;
22 if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then
23 cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled &amp;&amp;
24 cp -p $BUNDLED_LGF_FQSO ${BUNDLED_LGF_FQSO}.bundled &amp;&amp;
25 cp -p $LGF_CANON $BUNDLED_LGF_CANON &amp;&amp;
26 cp -p $LGF_CANON $BUNDLED_LGF_FQSO
27 fi
11 </action> 28 </action>
12 <action type="set_environment"> 29 <action type="set_environment">
13 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable> 30 <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> 31 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
15 </action> 32 </action>
24 </package> 41 </package>
25 <package name="libpng" version="1.6.7"> 42 <package name="libpng" version="1.6.7">
26 <repository changeset_revision="05df724aefbb" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 43 <repository changeset_revision="05df724aefbb" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
27 </package> 44 </package>
28 <package name="cairo" version="1.12.14"> 45 <package name="cairo" version="1.12.14">
29 <repository changeset_revision="8294add5c76e" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 46 <repository changeset_revision="3d4edf152b1b" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
30 </package> 47 </package>
31 <package name="pixman" version="0.32.6"> 48 <package name="pixman" version="0.32.6">
32 <repository changeset_revision="b67e27ea8bd3" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 49 <repository changeset_revision="06f701aa92e2" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
33 </package> 50 </package>
34 <package name="freetype" version="2.5.2"> 51 <package name="freetype" version="2.5.2">
35 <repository changeset_revision="ee307f3ce5dc" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 52 <repository changeset_revision="3b09e7916896" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
36 </package> 53 </package>
37 <package name="ncurses" version="6.0"> 54 <package name="ncurses" version="6.0">
38 <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 55 <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
39 </package> 56 </package>
40 <package name="fontconfig" version="2.11.1"> 57 <package name="fontconfig" version="2.11.1">
41 <repository changeset_revision="b20e4c53891e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 58 <repository changeset_revision="2ce32675340e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
42 </package> 59 </package>
43 <action type="set_environment_for_install"> 60 <action type="set_environment_for_install">
44 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> 61 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
45 <package name="readline" version="6.3" /> 62 <package name="readline" version="6.3" />
46 </repository> 63 </repository>
47 <repository changeset_revision="05df724aefbb" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> 64 <repository changeset_revision="05df724aefbb" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
48 <package name="libpng" version="1.6.7" /> 65 <package name="libpng" version="1.6.7" />
49 </repository> 66 </repository>
50 <repository changeset_revision="8294add5c76e" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> 67 <repository changeset_revision="3d4edf152b1b" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
51 <package name="cairo" version="1.12.14" /> 68 <package name="cairo" version="1.12.14" />
52 </repository> 69 </repository>
53 <repository changeset_revision="b67e27ea8bd3" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> 70 <repository changeset_revision="06f701aa92e2" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
54 <package name="pixman" version="0.32.6" /> 71 <package name="pixman" version="0.32.6" />
55 </repository> 72 </repository>
56 <repository changeset_revision="ee307f3ce5dc" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> 73 <repository changeset_revision="3b09e7916896" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
57 <package name="freetype" version="2.5.2" /> 74 <package name="freetype" version="2.5.2" />
58 </repository> 75 </repository>
59 <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> 76 <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
60 <package name="ncurses" version="6.0" /> 77 <package name="ncurses" version="6.0" />
61 </repository> 78 </repository>
62 <repository changeset_revision="b20e4c53891e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> 79 <repository changeset_revision="2ce32675340e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
63 <package name="fontconfig" version="2.11.1" /> 80 <package name="fontconfig" version="2.11.1" />
64 </repository> 81 </repository>
65 </action> 82 </action>
66 <action type="shell_command"> 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>
67 export LDFLAGS="-L$LIBPNG_LIB_PATH -L$PNG_LIBS -L$NCURSES_LIB_PATH -L$READLINE_LIB_PATH" &amp;&amp;
68 export LDFLAGS="$LDFLAGS -Wl,-rpath,$NCURSES_LIB_PATH" &amp;&amp;
69 export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &amp;&amp;
70 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &amp;&amp;
71 export LDFLAGS="$LDFLAGS -Wl,-rpath,$LIBPNG_LIB_PATH" &amp;&amp;
72 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
73 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FONTCONFIG_LIB_PATH" &amp;&amp;
74 export LDFLAGS="$LDFLAGS -Wl,-rpath,$CAIRO_LIB_PATH" &amp;&amp;
75 export CFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &amp;&amp;
76 export CXXFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &amp;&amp;
77 export CPPFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &amp;&amp;
78 ./configure --with-tcltk \
79 --with-blas \
80 --with-lapack \
81 --with-readline \
82 --with-cairo \
83 --with-libpng \
84 --without-x \
85 --enable-R-shlib \
86 --disable-R-framework \
87 --libdir=$INSTALL_DIR/lib \
88 --prefix=$INSTALL_DIR
89 </action>
90 <action type="make_install" /> 84 <action type="make_install" />
91 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action> 85 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
92 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action> 86 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
93 </actions> 87 </actions>
94 <action type="set_environment"> 88 <action type="set_environment">