Mercurial > repos > nilesh > sickle

changeset 3:be04ffa66753

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merged zlib and sickle library
author nilesh
date Fri, 12 Jul 2013 20:08:05 -0500
parents 9159a1bf8615
children 29af9584ed26
files sickle.xml tool_dependencies.xml
diffstat 2 files changed, 3 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/sickle.xml	Fri Jul 12 16:07:31 2013 -0500
+++ b/sickle.xml	Fri Jul 12 20:08:05 2013 -0500
@@ -1,7 +1,6 @@
 <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>
--- a/tool_dependencies.xml	Fri Jul 12 16:07:31 2013 -0500
+++ b/tool_dependencies.xml	Fri Jul 12 20:08:05 2013 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="zlib" version="1.2.8">
-        <install version="1.0">
+    <package name="sickle" version="1.21.0">
+        <install version="1.1">
             <actions>
                 <action type="download_by_url">http://zlib.net/zlib-1.2.8.tar.gz</action>
                 <action type="shell_command">./configure --prefix=$INSTALL_DIR/zlib</action>
@@ -10,20 +10,8 @@
                 <action type="set_environment">
                     <environment_variable name="ZLIB_PATH" action="set_to">$INSTALL_DIR/zlib/lib</environment_variable>
                 </action>
-                <action type="set_environment">
-                    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/zlib/lib</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        	zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. The zlib data format is itself portable across platforms.
-        </readme>
-    </package>
-    <package name="sickle" version="1.21.0">
-        <install version="1.0">
-            <actions>
                 <action type="shell_command">git clone https://github.com/najoshi/sickle.git</action>
-                <action type="shell_command">make LIBS="-L$ZLIB_PATH -lz"</action>
+                <action type="shell_command">make LIBS="-L$INSTALL_DIR/zlib/lib -lz"</action>
                 <action type="move_file">
                     <source>sickle</source>
                     <destination>$INSTALL_DIR/bin</destination>