changeset 4:6d875183e6f7

Another attempt to fix broken tar upload functionality of toolshed.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.txt	Wed Jul 24 13:33:50 2013 -0400
@@ -0,0 +1,14 @@
+This tool uses the sambamba view command to filter BAM/SAM on flags, fields, tags, and region. Input is SAM or BAM file.
+
+There are a three options for installation of sambamba:
+
+	1) Automated toolshed installation.  This requires that a D2 compiler (dmd >= 2.063) is installed.  The automated installation will attempt to use the dmd compiler and thus **will not be optimized**.  
+
+	2) Manual compilation.  For performance reasons, the sambamba developers recommend you use either GDC or LDC as they use GCC and LLVM backends and do a much better job at optimization.  You should then use the sambamba-ldmd2-64 make target.  See https://github.com/lomereiter/sambamba/wiki/Command-line-tools for more information.
+
+	3) Precompiled binary (recommended).  You may wish to simply use a precompiled binary of sambamba available at https://www.dropbox.com/sh/v05fsb5aarob3xe/iUHgyud31a/sambamba.  
+
+If you choose option 2 or 3, sambamba may be installed as a "Managed Dependency" in Galaxy's "tool_dependency_dir".  See http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies. 
+
+The development repository for the galaxy wrapper is at: https://bitbucket.org/lance_parsons/sambamba_filter_galaxy_wrapper
+The sambamba development repository is at: https://github.com/lomereiter/sambamba.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Jul 24 13:33:50 2013 -0400
@@ -0,0 +1,36 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="sambamba" version="0.3.3">
+        <install version="1.0">
+            <actions>
+				<action type="shell_command">git clone --recursive https://github.com/lomereiter/sambamba</action>
+                <action type="shell_command">git checkout v0.3.3</action>
+                <action type="shell_command">git submodule update --recursive</action>
+                <action type="shell_command">make release</action>
+                <action type="move_directory_files">
+                    <source_directory>build</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+		</install>
+		<readme>
+ This tool uses the sambamba view command to filter BAM/SAM on flags, fields, tags, and region. Input is SAM or BAM file.
+
+There are a three options for installation of sambamba:
+
+	1) Automated toolshed installation.  This requires that a D2 compiler (dmd >= 2.063) is installed.  The automated installation will attempt to use the dmd compiler and thus **will not be optimized**.  
+
+	2) Manual compilation.  For performance reasons, the sambamba developers recommend you use either GDC or LDC as they use GCC and LLVM backends and do a much better job at optimization.  You should then use the sambamba-ldmd2-64 make target.  See https://github.com/lomereiter/sambamba/wiki/Command-line-tools for more information.
+
+	3) Precompiled binary (recommended).  You may wish to simply use a precompiled binary of sambamba available at https://www.dropbox.com/sh/v05fsb5aarob3xe/iUHgyud31a/sambamba.  
+
+If you choose option 2 or 3, sambamba may be installed as a "Managed Dependency" in Galaxy's "tool_dependency_dir".  See http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies. 
+
+The development repository for the galaxy wrapper is at: https://bitbucket.org/lance_parsons/sambamba_filter_galaxy_wrapper.
+The sambamba development repository is at: https://github.com/lomereiter/sambamba.
+        </readme>
+    </package>
+</tool_dependency>