changeset 89:a92c2ae342c4 draft

Uploaded

--- a/tool_dependencies.xml	Thu Nov 05 06:09:01 2015 -0500
+++ b/tool_dependencies.xml	Thu Nov 05 08:21:31 2015 -0500
@@ -1,49 +1,13 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="ncurses" version="6.0">
-        <repository changeset_revision="7fae9c4b2d10" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    
-    <package name="samtools_parallel_mpileup_0_1_19a" version="0.1.19a">
-        <install version="1.0">
-            <actions>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="387c0609c0b7" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="ncurses" version="5.9" />
-                    </repository>
-                </action>
-                
-                <action type="shell_command">
-                    svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup ;
-                    
-                    cd samtools-parallel-mpileup ;
-                    cd $(ls |grep samtools-) ;
-                    
-                    sed -i 's/-lcurses/-lncurses/' Makefile ;
-                    sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile ;
-                    
-                    make ;
-                    cp samtools ../samtools-parallel-mpileup
-                </action>
-                <action type="move_file">
-                    <source>samtools-parallel-mpileup/samtools-parallel-mpileup</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            Downloads and installs a modified version of samtools, able to paralellize the mpileup function.
-        </readme>
+
+    <package name="samtools_parallel_mpileup" version="0.1.19-a">
+        <repository changeset_revision="8eea1a2bd1f2" name="package_samtools_parallel_mpileup_0_1_19_a" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    
+
     <package name="varscan" version="2.3.6">
         <repository changeset_revision="f82940004c84" name="varscan_version_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>