Mercurial > repos > geert-vandeweyer > package_velvet
changeset 0:688d46996f1e draft
Uploaded
| author | geert-vandeweyer |
|---|---|
| date | Mon, 28 Jul 2014 05:41:10 -0400 |
| parents | |
| children | b4a34f56778b |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 32 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jul 28 05:41:10 2014 -0400 @@ -0,0 +1,32 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="velvet" version="1.2.10"> + <install version="1.0"> + <actions> + <action type="shell_command">git clone git://github.com/dzerbino/velvet.git</action> + <action type="make_directory">$INSTALL_DIR/bin</action> + <action type="shell_command">make 'OPENMP=1' 'LONGSEQUENCES=1' </action> + <action type="move_file"><source>velveth</source><destination>$INSTALL_DIR/bin</destination></action> + <action type="move_file"><source>velvetg</source><destination>$INSTALL_DIR/bin</destination></action> + + <action type="set_environment"> + <environment_variable action="set_to" name="OMP_THREAD_LIMIT">1</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +Galaxy tool_dependency for VELVET +================================= + +This tool_dependency is written by Geert Vandeweyer. VELVET is installed from github. As of writing, the version was 1.2.10 + +This package downloads, compiles and adds velvetg and velveth to <$PATH>. Enabled compiling options are: + +- OPENMP : allow multithreading. Set the number of threads in <tool_dependency_dir>/environment_settings/OMP_THREAD_LIMIT/geert-vandeweyer/package_velvet/<hash_string>/env.sh +- LONGSEQUENCES : allow long (>32kb) contigs + + + </readme> + </package> +</tool_dependency>