Mercurial > repos > s-kaufmann > synteny_mapper

comparison tool_dependencies.xml @ 15:9a495fd2fe0f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author s-kaufmann
date Fri, 15 Aug 2014 10:19:49 -0400
parents acb6cae8bfec
children a6af076506eb
comparison
equal deleted inserted replaced
14:acb6cae8bfec 15:9a495fd2fe0f
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <set_environment version="1.0"> 3 <package name="R_3_0_2" version="3.0.2">
4 <environment_variable name="JAR_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
5 </set_environment>
6
7 <set_environment version="1.0">
8 <environment_variable name="CIRCOS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
9 </set_environment>
10
11 <package name="circos" version="0.64">
12 <install version="1.0"> 4 <install version="1.0">
13 <actions> 5 <actions_group>
14 <!-- Downloads the Circos software from its website and unpacks it --> 6 <actions architecture="x86_64" os="darwin">
15 <action type="download_by_url">http://circos.ca/distribution/circos-0.64.tgz </action> 7 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.0.2-Darwin-x86_64.tgz</action>
16 <action type="move_directory_files"> 8 <action type="move_directory_files">
17 <source_directory>.</source_directory> 9 <source_directory>.</source_directory>
18 <destination_directory>$INSTALL_DIR/</destination_directory> 10 <destination_directory>$INSTALL_DIR</destination_directory>
19 </action> 11 </action>
20 <action type="set_environment"> 12 </actions>
21 <environment_variable name="CIRCOS_PATH" action="set_to">$INSTALL_DIR</environment_variable> 13 <actions architecture="x86_64" os="linux">
22 </action> 14 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/R/R-3.0.2-Linux-x86_64.tgz</action>
23 </actions> 15 <action type="move_directory_files">
16 <source_directory>.</source_directory>
17 <destination_directory>$INSTALL_DIR</destination_directory>
18 </action>
19 <action type="set_environment">
20 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
21 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
22 </action>
23 </actions>
24 <actions>
25 <package name="readline" version="6.2">
26 <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
27 </package>
28 <package name="libpng" version="1.6.7">
29 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
30 </package>
31 <package name="cairo" version="1.12.14">
32 <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
33 </package>
34 <package name="pixman" version="0.32.4">
35 <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
36 </package>
37 <package name="freetype" version="2.5.2">
38 <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
39 </package>
40 <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.0.2.tar.gz</action>
41 <action type="set_environment_for_install">
42 <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
43 <package name="readline" version="6.2" />
44 </repository>
45 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
46 <package name="libpng" version="1.6.7" />
47 </repository>
48 <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
49 <package name="cairo" version="1.12.14" />
50 </repository>
51 <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
52 <package name="pixman" version="0.32.4" />
53 </repository>
54 <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
55 <package name="freetype" version="2.5.2" />
56 </repository>
57 </action>
58 <action type="shell_command">
59 export LDFLAGS="-L$PNG_LIBS -L$READLINE_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$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
65 export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
66 export CPPFLAGS="-I$PNG_INCLUDES -I$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 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
81 <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
82 </actions>
83 <action type="set_environment">
84 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
85 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
86 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
87 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
88 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
89 </action>
90 </actions_group>
24 </install> 91 </install>
25 <readme> 92 <readme>
26 Downloads and installs Circos (v.0.64) for use in visualization. Requires perl to be installed. 93 The precompiled versions were built 2014-03-07.
94 R is a free software environment for statistical computing and graphics. http://www.r-project.org/
27 </readme> 95 </readme>
28 </package>
29
30 <set_environment version="1.0">
31 <environment_variable name="R_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
32 </set_environment>
33
34 <package name="R_3_0_2" version="3.0.2">
35 <install version="1.0">
36 <actions>
37 <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.2.tar.gz</action>
38 <action type="set_environment_for_install">
39 <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
40 <package name="readline" version="6.2" />
41 </repository>
42 <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
43 <package name="ncurses" version="5.9" />
44 </repository>
45 <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
46 <package name="libpng" version="1.6.7" />
47 </repository>
48 </action>
49
50 <action type="shell_command">
51 ./configure CPPFLAGS="-I$READLINE_INCLUDE_PATH -I${LIBPNG_ROOT}/include" LDFLAGS="-L$READLINE_LIB_PATH -L$NCURSES_LIB_PATH -L${LIBPNG_ROOT}/lib -lreadline -lncurses" --with-libpng --enable-R-shlib --with-x=no --libdir=$INSTALL_DIR/lib/ --bindir=$INSTALL_DIR --datarootdir=$INSTALL_DIR/share/
52 </action>
53
54 <action type="shell_command">make</action>
55 <action type="shell_command">make install</action>
56 <action type="set_environment">
57 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
58 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
59 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
60 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
61 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
62 <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
63 </action>
64 </actions>
65 </install>
66 <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme>
67 </package> 96 </package>
68
69 </tool_dependency> 97 </tool_dependency>