Mercurial > repos > lparsons > sambamba_filter
diff tool_dependencies.xml @ 0:80ed79e80b4a draft
Uploaded
| author | lparsons |
|---|---|
| date | Tue, 23 Jul 2013 16:19:11 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jul 23 16:19:11 2013 -0400 @@ -0,0 +1,29 @@ +<?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</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> + Sambamba requires a D2 compiler (dmd >= 2.062). The automated installation will attempt to use the dmd compiler and thus will not be optimized. + + 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. + + You may wish to simply use a precompiled binary of sambamba available at https://www.dropbox.com/sh/v05fsb5aarob3xe/iUHgyud31a/sambamba. This may be installed as a "Managed Dependency" in Galaxy's "tool_dependency_dir". See http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies. + + See the sambamba repository on github for complete details: https://github.com/lomereiter/sambamba. + </readme> + </package> +</tool_dependency>