Mercurial > repos > nilesh > sickle_dev2

changeset 1:0f95d40cb684

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first commit
author nilesh
date Mon, 15 Jul 2013 12:09:37 -0500
parents 9e66123d34e8
children 8df4a4096ae2
files tool_dependencies.xml
diffstat 1 files changed, 25 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jul 15 12:09:37 2013 -0500
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="sickle" version="1.21.0">
+        <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 --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$INSTALL_DIR/zlib/lib -lz"</action>
+                <action type="move_file">
+                    <source>sickle/sickle</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</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>
+</tool_dependency>