# HG changeset patch
# User bgruening
# Date 1432148387 14400
# Node ID 833c4be8f4d449123b7868ecf7e737de1e6b54aa

Imported from capsule None

diff -r 000000000000 -r 833c4be8f4d4 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed May 20 14:59:47 2015 -0400
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="pear" version="0.9.6">
+        <install version="1.0">
+            <actions_group>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://sco.h-its.org/exelixis/web/software/pear/files/pear-0.9.6-bin-64.tar.gz</action>
+                    <action type="move_file">
+                        <source>pear-0.9.6-bin-64</source>
+                        <destination>$INSTALL_DIR/bin/</destination>
+                    </action>
+                    <action type="shell_command">mv $INSTALL_DIR/bin/pear-0.9.6-bin-64 $INSTALL_DIR/bin/pear</action>
+                </actions>
+                <actions architecture="x86_64" os="darwin">
+                   <action type="download_by_url">http://sco.h-its.org/exelixis/web/software/pear/files/pear-0.9.6-src.tar.gz</action>
+                    <action type="autoconf" />
+                </actions>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="PEAR_ROOT_DIR">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>PEAR - Paired-End reAd mergeR
+        PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. 
+        It is fully parallelized and can run with as low as just a few kilobytes of memory.
+
+        PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input.
+        In addition, it implements a statistical test for minimizing false-positive results.
+        Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.
+        </readme>
+    </package>
+</tool_dependency>