# HG changeset patch
# User devteam
# Date 1386797017 18000
# Node ID cf998ddc0542ce91acce0967f513bd149004a553

Uploaded tool dependency definition.

diff -r 000000000000 -r cf998ddc0542 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Dec 11 16:23:37 2013 -0500
@@ -0,0 +1,94 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="emboss" version="5.0.0">
+        <install version="1.0">
+            <actions_group>
+                <actions architecture="i386" os="linux">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/emboss/emboss-5.0.0-Linux-i686.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>       
+                </actions>                
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/emboss/emboss-5.0.0-Linux-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>       
+                </actions>                
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/emboss/emboss-5.0.0-Darwin-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>       
+                </actions>                
+                <actions>
+                    <package name="libx11" version="1.5.0">
+                        <repository changeset_revision="bfb1f66b1402" name="package_libx11_1_5_0" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="libgd" version="2.1.0">
+                        <repository changeset_revision="3918b86c4f1f" name="package_libgd_2_1_0" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="libxproto" version="7.0.23">
+                        <repository changeset_revision="6a512bc84b0d" name="package_libxproto_7_0_23" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="libxcb" version="1.9.1">
+                        <repository changeset_revision="283d04f807f7" name="package_libxcb_1_9_1" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+                    </package>
+                    <action type="download_by_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/EMBOSS-5.0.0.tar.gz</action>
+                    <action type="set_environment_for_install">
+                        <repository changeset_revision="3918b86c4f1f" name="package_libgd_2_1_0" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
+                            <package name="libgd" version="2.1.0" />
+                        </repository>
+                        <repository changeset_revision="bfb1f66b1402" name="package_libx11_1_5_0" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
+                            <package name="libx11" version="1.5.0" />
+                        </repository>
+                        <repository changeset_revision="6a512bc84b0d" name="package_libxproto_7_0_23" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
+                            <package name="libxproto" version="7.0.23" />
+                        </repository>
+                        <repository changeset_revision="283d04f807f7" name="package_libxcb_1_9_1" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
+                            <package name="libxcb" version="1.9.1" />
+                        </repository>
+                    </action>
+                    <action type="shell_command">
+                        export LDFLAGS="-L$XCB_LIBS -lm"
+                        export CFLAGS="-I$XPROTO_INCLUDES" &amp;&amp; \
+                        ./configure --prefix=$INSTALL_DIR \
+                        --x-includes=$X11_INCLUDE_DIR \
+                        --x-libraries=$X11_LIB_DIR \
+                        --with-pngdriver=$GD_ROOT
+                    </action>
+                    <action type="shell_command">make &amp;&amp; make install</action>
+                    <action extract="true" type="download_file">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/PHYLIP-3.6b.tar.gz</action>
+                    <action type="change_directory">PHYLIP-3.6b</action>
+                    <action type="shell_command">
+                        export LDFLAGS="-L$XCB_LIBS -lm"
+                        export CFLAGS="-I$XPROTO_INCLUDES" &amp;&amp; \
+                        ./configure --prefix=$INSTALL_DIR \
+                        --x-includes=$X11_INCLUDE_DIR \
+                        --x-libraries=$X11_LIB_DIR \
+                        --with-pngdriver=$GD_ROOT
+                    </action>
+                    <action type="shell_command">make &amp;&amp; make install</action>
+                </actions>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="EMBOSS_ACDROOT">$INSTALL_DIR/share/EMBOSS/acd</environment_variable>
+                    <environment_variable action="set_to" name="EMBOSS_DATA">$INSTALL_DIR/share/EMBOSS/data</environment_variable>
+                    <environment_variable action="set_to" name="PLPLOT_LIB">$INSTALL_DIR/share/EMBOSS</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>
+These links provide information for building the Emboss package in most environments.
+
+System requirements
+http://emboss.sourceforge.net/download/#Requirements
+
+Platform-dependent notes
+http://emboss.sourceforge.net/download/#Platforms
+        </readme>
+    </package>
+</tool_dependency>