Mercurial > repos > iuc > package_r_3_2_1
comparison tool_dependencies.xml @ 2:2ce7fd67f394 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
author | iuc |
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date | Thu, 03 Dec 2015 07:23:45 -0500 |
parents | fae49a02a848 |
children | d0bf97420fb5 |
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1:fae49a02a848 | 2:2ce7fd67f394 |
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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=$INSTALL_DIR/lib/libgfortran.so.3.0.0 && | |
15 BUNDLED_LGF_FQSO=$INSTALL_DIR/lib/libgfortran.so.3 && | |
16 BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` && | |
17 echo 'program test; end program test' > test.f90 && | |
18 gfortran -o test test.f90 && | |
19 LGF=`ldd test | grep libgfortran | awk '{print $3}'` && | |
20 LGF_CANON=`readlink -f $LGF` && | |
21 LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` && | |
22 if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then | |
23 cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled && | |
24 cp -p $BUNDLED_LGF_FQSO ${BUNDLED_LGF_FQSO}.bundled && | |
25 cp -p $LGF_CANON $BUNDLED_LGF_CANON && | |
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" && | |
68 export LDFLAGS="$LDFLAGS -Wl,-rpath,$NCURSES_LIB_PATH" && | |
69 export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" && | |
70 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" && | |
71 export LDFLAGS="$LDFLAGS -Wl,-rpath,$LIBPNG_LIB_PATH" && | |
72 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" && | |
73 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FONTCONFIG_LIB_PATH" && | |
74 export LDFLAGS="$LDFLAGS -Wl,-rpath,$CAIRO_LIB_PATH" && | |
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" && | |
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" && | |
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" && | |
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"> |