diff tool_dependencies.xml @ 4:98e35d7ce5c9

sickle now refers to zlib in its own directory

--- a/tool_dependencies.xml	Wed Jul 10 00:16:36 2013 -0400
+++ b/tool_dependencies.xml	Fri Jul 12 13:49:15 2013 -0500
@@ -3,25 +3,28 @@
     <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>
-                <action type="shell_command">./configure</action>
-                 <action type="shell_command">./configure --prefix=$INSTALL_DIR/zlib</action>
+                <action type="download_by_url">http://zlib.net/zlib-1.2.8.tar.gz</action>
+                <action type="shell_command">./configure --prefix=$INSTALL_DIR/zlib</action>
                 <action type="shell_command">make</action>
                 <action type="shell_command">make install prefix=$INSTALL_DIR/zlib</action>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="ZLIB_PATH" action="set_to">$INSTALL_DIR/zlib/lib</environment_variable>
+                </action>
+            </actions>
+                <action type="set_environment">
+                    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/zlib/lib</environment_variable>
                 </action>
             </actions>
         </install>
         <readme>
-        	Tabix version 0.2.6. Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching.
+        	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="1.2.8">
+    <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</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>
@@ -32,7 +35,7 @@
             </actions>
         </install>
         <readme>
-            Tabix version 0.2.6. Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching.
+            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>
 </tool_dependency>