# HG changeset patch
# User s-kaufmann
# Date 1408112797 14400
# Node ID a6af076506eb752cac0e85dd2fd540b5f70ea3d5
# Parent  9a495fd2fe0f35c6b1d8620dfe38041ac236b354
Uploaded

diff -r 9a495fd2fe0f -r a6af076506eb tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Aug 15 10:19:49 2014 -0400
+++ b/tool_dependencies.xml	Fri Aug 15 10:26:37 2014 -0400
@@ -1,97 +1,38 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="R_3_0_2" version="3.0.2">
+    <set_environment version="1.0">
+        <environment_variable name="JAR_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>   
+    </set_environment>
+
+    <set_environment version="1.0">
+	<environment_variable name="CIRCOS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+
+<package name="circos" version="0.64">
         <install version="1.0">
-            <actions_group>
-                <actions architecture="x86_64" os="darwin">
-                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.0.2-Darwin-x86_64.tgz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
-                <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/R/R-3.0.2-Linux-x86_64.tgz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                    <action type="set_environment">
-                        <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
-                        <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
-                    </action>
-                </actions>
-                <actions>
-                    <package name="readline" version="6.2">
-                        <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-                    </package>
-                    <package name="libpng" version="1.6.7">
-                        <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-                    </package>
-                    <package name="cairo" version="1.12.14">
-                        <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-                    </package>
-                    <package name="pixman" version="0.32.4">
-                        <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-                    </package>
-                    <package name="freetype" version="2.5.2">
-                        <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-                    </package>
-                    <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.0.2.tar.gz</action>
-                    <action type="set_environment_for_install">
-                        <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                            <package name="readline" version="6.2" />
-                        </repository>
-                        <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                            <package name="libpng" version="1.6.7" />
-                        </repository>
-                        <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                            <package name="cairo" version="1.12.14" />
-                        </repository>
-                        <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                            <package name="pixman" version="0.32.4" />
-                        </repository>
-                        <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                            <package name="freetype" version="2.5.2" />
-                        </repository>
-                    </action>
-                    <action type="shell_command">
-                        export LDFLAGS="-L$PNG_LIBS -L$READLINE_LIB_PATH" &amp;&amp;
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &amp;&amp;
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &amp;&amp;
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" &amp;&amp;
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
-                        export CFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
-                        export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
-                        export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
-                        ./configure --with-tcltk \
-                                    --with-blas \
-                                    --with-lapack \
-                                    --with-readline \
-                                    --with-cairo \
-                                    --with-libpng \
-                                    --without-x \
-                                    --enable-R-shlib \
-                                    --disable-R-framework \
-                                    --libdir=$INSTALL_DIR/lib \
-                                    --prefix=$INSTALL_DIR 
-                    </action>
-                    <action type="make_install" />
-                    <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
-                    <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
-                </actions>
-                <action type="set_environment">
-                    <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
-                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
-                    <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
-                    <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions_group>
+            <actions>          
+               <!-- Downloads the Circos software from its website and unpacks it -->
+               <action type="download_by_url">http://circos.ca/distribution/circos-0.64.tgz </action>
+               <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR/</destination_directory>
+               </action>                
+               <action type="set_environment">
+                        <environment_variable name="CIRCOS_PATH" action="set_to">$INSTALL_DIR</environment_variable>
+                </action>                            
+            </actions>
         </install>
         <readme>
-        The precompiled versions were built 2014-03-07.       
-        R is a free software environment for statistical computing and graphics. http://www.r-project.org/
+Downloads and installs Circos (v.0.64) for use in visualization. Requires perl to be installed.
         </readme>
-    </package>
+    </package>  
+
+    <set_environment version="1.0">
+	<environment_variable name="R_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+
+    <package name="package_r_3_0_2" version="3.0.2">
+                        <repository changeset_revision="50f7e1e71271" name="package_r_3_0_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+                    </package>
+
 </tool_dependency>