Mercurial > repos > nilesh > sickle_dev

changeset 8:7ebde7d1281c

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merged dependencies
author nilesh
date Mon, 15 Jul 2013 11:50:25 -0500
parents 7e599ffef625
children 30f36c4faa39
files sickle.xml tool_dependencies.xml
diffstat 2 files changed, 5 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/sickle.xml	Mon Jul 15 11:26:46 2013 -0500
+++ b/sickle.xml	Mon Jul 15 11:50:25 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	Mon Jul 15 11:26:46 2013 -0500
+++ b/tool_dependencies.xml	Mon Jul 15 11:50:25 2013 -0500
@@ -1,22 +1,14 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="zlib" version="1.2.8">
-        <repository changeset_revision="28f618926504" name="zlib" owner="nilesh" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
     <package name="sickle" version="1.21.0">
         <install version="1.0">
             <actions>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="28f618926504" name="zlib" owner="nilesh" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="zlib" version="1.2.8" />
-                   </repository>
-                </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="shell_command">git clone https://github.com/najoshi/sickle.git</action>
-                <action type="shell_command">cd ./sickle &amp;&amp; make LIBS="-L$ENV[ZLIB_PATH] -lz"</action>
-                <action type="move_file">
-                    <source>sickle</source>
-                    <destination>.</destination>
-                </action>
+                <action type="shell_command">cd ./sickle &amp;&amp; make LIBS="-L$INSTALL_DIR/zlib/lib -lz"</action>
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                 </action>