# HG changeset patch
# User nilesh
# Date 1373903262 18000
# Node ID b04d24abd5734b4c0a7a4e3f61aae88416233745
# Parent  db0c767dbe0954da7614bdbc21be8a07c835e35a
separated into two dependencies

diff -r db0c767dbe09 -r b04d24abd573 sickle.xml
--- a/sickle.xml	Mon Jul 15 10:11:13 2013 -0500
+++ b/sickle.xml	Mon Jul 15 10:47:42 2013 -0500
@@ -1,6 +1,7 @@
 <tool id="sickle" name="Sickle">
 	<description>Windowed Adaptive Trimming of FastQ data</description>
 	<requirements>
+		<requirement type="package" version="1.2.8">zlib</requirement>
 		<requirement type="package" version="1.21.0">sickle</requirement>
 	</requirements>
 	<command>
diff -r db0c767dbe09 -r b04d24abd573 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jul 15 10:11:13 2013 -0500
+++ b/tool_dependencies.xml	Mon Jul 15 10:47:42 2013 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="sickle" version="1.21.0">
+    <package name="zlib" version="1.2.8">
         <install version="1.0">
             <actions>
                 <action type="download_by_url">http://zlib.net/zlib-1.2.8.tar.gz</action>
@@ -10,8 +10,17 @@
                 <action type="set_environment">
                     <environment_variable name="ZLIB_PATH" action="set_to">$INSTALL_DIR/zlib/lib</environment_variable>
                 </action>
+            </actions>
+        </install>
+        <readme>
+            Sickle requires a C compiler; GCC or clang are recommended. Sickle relies on Heng Li's kseq.h, which is bundled with the source. It also requires zlib, which is included in this repo.
+        </readme>
+    </package>
+        <package name="sickle" version="1.21.0">
+        <install version="1.0">
+            <actions>
                 <action type="shell_command">git clone https://github.com/najoshi/sickle.git</action>
-                <action type="shell_command">make LIBS="-L$INSTALL_DIR/zlib/lib -lz"</action>
+                <action type="shell_command">make LIBS="-L$ENV[ZLIB_PATH] -lz"</action>
                 <action type="move_file">
                     <source>sickle</source>
                     <destination>$INSTALL_DIR/bin</destination>