# HG changeset patch
# User iuc
# Date 1435490615 14400
# Node ID 047eb877b6f0c8918279e6972509fa3fe6331a76
# Parent  507901240749923d3e3b1a0bb4beeca01d3bd538
Uploaded

diff -r 507901240749 -r 047eb877b6f0 bismark_bowtie2_wrapper.xml
--- a/bismark_bowtie2_wrapper.xml	Wed Feb 11 16:21:27 2015 -0500
+++ b/bismark_bowtie2_wrapper.xml	Sun Jun 28 07:23:35 2015 -0400
@@ -1,11 +1,10 @@
-<tool id="bismark_bowtie2" name="Bismark" version="0.10.2">
+<tool id="bismark_bowtie2" name="Bismark" version="0.14.3">
     <!-- Wrapper compatible with Bismark version 0.10 -->
     <description>bisulfite mapper (bowtie2)</description>
     <!--<version_command>bismark version</version_command>-->
     <requirements>
-        <requirement type="set_environment">SCRIPT_PATH</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
-        <requirement type="package" version="2.1.0">bowtie2</requirement>
+        <requirement type="package" version="2.2.5">bowtie2</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -20,7 +19,7 @@
         ## Change this to accommodate the number of threads you have available.
         --num-threads "\${GALAXY_SLOTS:-24}"
 
-        --bismark_path \$SCRIPT_PATH
+        --bismark_path $__tool_directory__
 
         --bowtie2
 
diff -r 507901240749 -r 047eb877b6f0 bismark_bowtie_wrapper.xml
--- a/bismark_bowtie_wrapper.xml	Wed Feb 11 16:21:27 2015 -0500
+++ b/bismark_bowtie_wrapper.xml	Sun Jun 28 07:23:35 2015 -0400
@@ -1,11 +1,10 @@
-<tool id="bismark_bowtie" name="Bismark" version="0.10.2">
+<tool id="bismark_bowtie" name="Bismark" version="0.14.3">
     <!-- Wrapper compatible with Bismark version 0.10 -->
     <description>bisulfite mapper (bowtie)</description>
     <!--<version_command>bismark version</version_command>-->
     <requirements>
-        <requirement type="set_environment">SCRIPT_PATH</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
-        <requirement type="package" version="0.12.8">bowtie</requirement>
+        <requirement type="package" version="1.0.0">bowtie</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -17,7 +16,7 @@
 <![CDATA[
         bismark_wrapper.py
 
-        --bismark_path \$SCRIPT_PATH
+        --bismark_path $__tool_directory__
 
         ##
         ## Bismark Genome Preparation, if desired.
diff -r 507901240749 -r 047eb877b6f0 bismark_methylation_extractor.xml
--- a/bismark_methylation_extractor.xml	Wed Feb 11 16:21:27 2015 -0500
+++ b/bismark_methylation_extractor.xml	Sun Jun 28 07:23:35 2015 -0400
@@ -1,11 +1,10 @@
-<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.10.2">
+<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.14.3">
     <!-- Wrapper compatible with Bismark version 0.10 -->
     <description>Reports on methylation status of reads mapped by Bismark</description>
     <!--<version_command>bismark_methylation_extractor version</version_command>-->
     <requirements>
-        <requirement type="set_environment">SCRIPT_PATH</requirement>
-        <requirement type="package" version="0.12.8">bowtie</requirement>
-        <requirement type="package" version="2.1.0">bowtie2</requirement>
+        <requirement type="package" version="1.0.0">bowtie</requirement>
+        <requirement type="package" version="2.2.5">bowtie2</requirement>
     </requirements>
     <parallelism method="basic"></parallelism>
     <command interpreter="python">
@@ -14,7 +13,7 @@
 
         --infile $input
 
-        --bismark_path \$SCRIPT_PATH
+        --bismark_path $__tool_directory__
 
         #if $singlePaired.sPaired == "single":
             --single-end
diff -r 507901240749 -r 047eb877b6f0 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Feb 11 16:21:27 2015 -0500
+++ b/tool_dependencies.xml	Sun Jun 28 07:23:35 2015 -0400
@@ -1,61 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <set_environment version="1.0">
-        <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-    <package name="bowtie2" version="2.1.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>bowtie2</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>bowtie2-align</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>bowtie2-build</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-Compiling bowtie2 requires zlib and libpthread to be present on your system.
-        </readme>
+    <package name="bowtie2" version="2.2.5">
+        <repository changeset_revision="e627be2bba58" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="bowtie" version="0.12.8">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.8/bowtie-0.12.8-src.zip</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>bowtie</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>bowtie-inspect</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>bowtie-build</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
+    <package name="bowtie" version="1.0.0">
+        <repository changeset_revision="0931da782b5d" name="package_bowtie_1_0_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>