Mercurial > repos > s-kaufmann > synteny_mapper

comparison tool_dependencies.xml @ 16:a6af076506eb draft

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Uploaded
author s-kaufmann
date Fri, 15 Aug 2014 10:26:37 -0400
parents 9a495fd2fe0f
children 98c0153c737a
comparison
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15:9a495fd2fe0f 16:a6af076506eb
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="R_3_0_2" version="3.0.2"> 3 <set_environment version="1.0">
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">
4 <install version="1.0"> 12 <install version="1.0">
5 <actions_group> 13 <actions>
6 <actions architecture="x86_64" os="darwin"> 14 <!-- Downloads the Circos software from its website and unpacks it -->
7 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.0.2-Darwin-x86_64.tgz</action> 15 <action type="download_by_url">http://circos.ca/distribution/circos-0.64.tgz </action>
8 <action type="move_directory_files"> 16 <action type="move_directory_files">
9 <source_directory>.</source_directory> 17 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR</destination_directory> 18 <destination_directory>$INSTALL_DIR/</destination_directory>
11 </action> 19 </action>
12 </actions> 20 <action type="set_environment">
13 <actions architecture="x86_64" os="linux"> 21 <environment_variable name="CIRCOS_PATH" action="set_to">$INSTALL_DIR</environment_variable>
14 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/R/R-3.0.2-Linux-x86_64.tgz</action> 22 </action>
15 <action type="move_directory_files"> 23 </actions>
16 <source_directory>.</source_directory>
17 <destination_directory>$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>
91 </install> 24 </install>
92 <readme> 25 <readme>
93 The precompiled versions were built 2014-03-07. 26 Downloads and installs Circos (v.0.64) for use in visualization. Requires perl to be installed.
94 R is a free software environment for statistical computing and graphics. http://www.r-project.org/
95 </readme> 27 </readme>
96 </package> 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="package_r_3_0_2" version="3.0.2">
35 <repository changeset_revision="50f7e1e71271" name="package_r_3_0_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
36 </package>
37
97 </tool_dependency> 38 </tool_dependency>