--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Nov 20 06:49:06 2015 -0500
@@ -0,0 +1,77 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="ncurses" version="5.9">
+        <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="zlib" version="1.2.8">
+        <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="trinity" version="2.0.6">
+        <install version="1.0">
+            <actions>
+                <action sha256sum="e0c3ec885fdcfe3422ea492372518ddf5d1aed3daa187c69c4254516b0845de1" type="download_by_url">https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.6.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="ncurses" version="5.9" />
+                    </repository>
+                    <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="zlib" version="1.2.8" />
+                    </repository>
+                </action>
+                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' trinity-plugins/Makefile</action>
+                <action type="shell_command">sed -i.bak -e 's/-ltinfo//' trinity-plugins/Makefile</action> <!-- tinfo is included in ncurses lib-->
+                <action type="shell_command">sed -i.bak -e '/tar -zxvf ${RSEM_CODE}.tar.gz/a \\tsed -i.bak -e "s|-lz|-lz -L${ZLIB_ROOT_PATH}/lib|" ${RSEM_CODE}/Makefile ${RSEM_CODE}/sam/Makefile' trinity-plugins/Makefile</action> <!-- In case you have an obsolete zlib in /usr/lib -->
+                <action type="shell_command">make</action>
+                <action type="shell_command">make plugins</action>
+
+                <action type="move_file">
+                    <source>Trinity</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>Analysis</source_directory>
+                    <destination_directory>$INSTALL_DIR/Analysis</destination_directory>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>Butterfly</source_directory>
+                    <destination_directory>$INSTALL_DIR/Butterfly</destination_directory>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>Chrysalis</source_directory>
+                    <destination_directory>$INSTALL_DIR/Chrysalis</destination_directory>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>Inchworm</source_directory>
+                    <destination_directory>$INSTALL_DIR/Inchworm</destination_directory>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>PerlLib</source_directory>
+                    <destination_directory>$INSTALL_DIR/PerlLib</destination_directory>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>trinity-plugins</source_directory>
+                    <destination_directory>$INSTALL_DIR/trinity-plugins</destination_directory>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>util</source_directory>
+                    <destination_directory>$INSTALL_DIR/util</destination_directory>
+                </action>
+
+                <action type="shell_command">rm $INSTALL_DIR/trinity-plugins/*tar.gz</action>
+
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/util</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/collectl/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/fastool</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/jellyfish/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/parafly/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/transdecoder</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/Trimmomatic</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/slclust/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/GAL_0.2.1</environment_variable>
+                </action>
+            </actions>
+        </install>
+    </package>
+</tool_dependency>