# HG changeset patch
# User bgruening
# Date 1393974804 18000
# Node ID 5f4562dc0890c2f5611016b2a77dd6261c3ff638
# Parent  4235fcb5b09054a3b51af584ce42f1bff982c0c6
Uploaded

diff -r 4235fcb5b090 -r 5f4562dc0890 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Mar 02 11:49:08 2014 -0500
+++ b/tool_dependencies.xml	Tue Mar 04 18:13:24 2014 -0500
@@ -1,31 +1,48 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="R_3_0_1" version="3.0.1">
-        <repository changeset_revision="4666f68ad4d5" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="libxml2" version="2.9.1">
+        <repository changeset_revision="cff446402e07" name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="iconv" version="1.14">
+        <repository changeset_revision="5b87c1521e4d" name="package_iconv_1_14" owner="iracooke" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="perl" version="5.18.1">
-        <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="openssl" version="1.0">
+        <repository changeset_revision="d3f9ae5d3727" name="package_openssl_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <set_environment version="1.0">
-        <environment_variable action="set_to" name="MICLIP_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-    <package name="miclip" version="1.2">
+
+    <package name="ruby" version="2.0">
         <install version="1.0">
             <actions>
-                <action type="setup_r_environment">
-                    <repository changeset_revision="4666f68ad4d5" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="R_3_0_1" version="3.0.1" />
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="cff446402e07" name="package_libxml2_2_9_1" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="libxml2" version="2.9.1" />
+                    </repository>
+                    <repository changeset_revision="5b87c1521e4d" name="package_iconv_1_14" owner="iracooke" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="iconv" version="1.14" />
+                    </repository>
+                    <repository changeset_revision="d3f9ae5d3727" name="package_openssl_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="openssl" version="1.0" />
                     </repository>
-                        <package>https://github.com/bgruening/download_store/raw/master/miclip/moments_0.13.tar.gz</package>
-                        <package>https://github.com/bgruening/download_store/raw/master/miclip/VGAM_0.9-3.tar.gz</package>
-                        <package>https://github.com/bgruening/download_store/raw/master/miclip/MiClip_1.2.tar.gz</package>
+                </action>
+
+                <action type="download_file">http://cache.ruby-lang.org/pub/ruby/2.0/ruby-2.0.0-p451.tar.gz</action>
+                <!-- Fails on OSX due to lack of openssl. -->
+                <action type="autoconf">--disable-install-doc</action>
+
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="RUBYLIB">$INSTALL_DIR/lib/</environment_variable>
+                    <environment_variable action="set_to" name="RUBY_HOME">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="GALAXY_RUBY_HOME">$INSTALL_DIR</environment_variable>
                 </action>
             </actions>
         </install>
         <readme>
-        MiClip: A Model-based Approach to Identify Binding Sites in CLIP-Seq Data
-        Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Here we present MiClip,a novel model-based approach to identify high-confidence protein-RNA binding sites in CLIP-Seq datasets. This approach assigns confidence value to each binding site on a probabilistic basis. The MiClip package can be flexibly applied to analyze both HITS-CLIP data and PAR-CLIP data.
-        http://cran.r-project.org/web/packages/MiClip/
+            This installs ruby 2.0.x. Ruby is a dynamic, open source programming language with a focus on simplicity and productivity.
+            It has an elegant syntax that is natural to read and easy to write.
+            https://www.ruby-lang.org/
+
+            RUBYHOME and RUBYLIB will be set and with GALAXY_RUBY_HOME you can access the root installation directory.
         </readme>
     </package>
 </tool_dependency>