# HG changeset patch
# User bgruening
# Date 1383439424 14400
# Node ID b738c51af1322c01148eb7c0da577adfb4af5218
# Parent  564b46e4fda7787ea909f7bdd5df418d3182968f
Uploaded

diff -r 564b46e4fda7 -r b738c51af132 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Jun 30 19:30:17 2013 -0400
+++ b/tool_dependencies.xml	Sat Nov 02 20:43:44 2013 -0400
@@ -1,52 +1,33 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="lapack" version="3.4.2">
-        <repository changeset_revision="a6b8f46acca7" name="package_lapack_3_4" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="atlas" version="3.10.1">
-        <repository changeset_revision="25dc49b0d6d5" name="package_atlas_3_10" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="readline" version="6.2">
-        <repository changeset_revision="782fae4417eb" name="package_readline_6_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-
-    <package name="R_3_0_1" version="3.0.1">
+    <package name="bioperl" version="1.6.922">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action>
+                <!-- install perl -->
+                <!--<action type="download_by_url">http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</action>-->
+                <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="25dc49b0d6d5" name="package_atlas_3_10" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="atlas" version="3.10.1" />
-                    </repository>
-                    <repository changeset_revision="a6b8f46acca7" name="package_lapack_3_4" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="lapack" version="3.4.2" />
-                    </repository>
-                    <repository changeset_revision="782fae4417eb" name="package_readline_6_2" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="readline" version="6.2" />
+                    <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="perl" version="5.18.1" />
                     </repository>
                 </action>
 
-                <!--
-                with-blas="$LAPACK_LIB_DIR"
-                with-lapack="-L$ATLAS_LIB_DIR -llapack -lcblas"
+                <action type="shell_command">cpanm --local-lib=$INSTALL_DIR XML::Parser</action>
+                <action type="shell_command">cpanm --local-lib=$INSTALL_DIR Bundle::BioPerl</action>
+
 
-                export BLAS=$LAPACK_LIB_DIR/libblas.a &amp;&amp; 
-                export LAPACK=$LAPACK_LIB_DIR/liblapack.a &amp;&amp; 
-                export ATLAS=$ATLAS_LIB_DIR/libatlas.a &amp;&amp; 
-LD_LIBRARY_PATH
-                -->
-                <action type="shell_command">
-                    export LD_LIBRARY_PATH=$READLINE_LIB_PATH &amp;&amp; 
-                    ./configure --with-lapack="-L$ATLAS_LIB_DIR -llapack -lcblas" --with-blas="$LAPACK_LIB_DIR" --enable-R-shlib  --with-x=no --with-readline=yes --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install
-                </action>
                 <action type="set_environment">
-                    <environment_variable action="set_to" name="R_HOME">$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/lib/R/bin</environment_variable>
-                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
+                    <environment_variable action="set_to" name="PERL_ROOT_DIR">$INSTALL_DIR/lib</environment_variable>
                 </action>
             </actions>
         </install>
-        <readme />
+        <readme>
+            Bundle::BioPerl
+        </readme>
     </package>
 </tool_dependency>