Mercurial > repos > jjohnson > package_velvet_1_2_10
changeset 0:378fc267bd0e draft default tip
Uploaded
| author | jjohnson |
|---|---|
| date | Thu, 25 Jul 2013 09:28:00 -0400 |
| parents | |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 45 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jul 25 09:28:00 2013 -0400 @@ -0,0 +1,45 @@ +<?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 velvet</action> + <action type="shell_command">git reset --hard 5cea317b4ec5c3f0fd2931321bc7231d8a250682</action> + <action type="shell_command">make -i CATEGORIES=4 MAXKMERLENGTH=191 OPENMP=1</action> + <action type="shell_command">mkdir scripts</action> + <action type="shell_command">find contrib/[a-z]* -type f -name '*.p?' -exec cp -p {} scripts ";"</action> + <action type="shell_command">cp -rp contrib/VelvetOptimiser*/VelvetOpt* scripts</action> + <action type="shell_command">ls scripts</action> + <action type="move_file"> + <source>velvetg</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>velveth</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_directory_files"> + <source_directory>scripts</source_directory> + <destination_directory>$INSTALL_DIR/scripts</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable> + </action> + <action type="set_environment"> + <environment_variable name="MAXKMERLENGTH" action="set_to">191</environment_variable> + </action> + <action type="set_environment"> + <environment_variable name="CATEGORIES" action="set_to">4</environment_variable> + </action> + </actions> + </install> + <readme> + Velvet is a sequence assembler for very short reads. + http://www.ebi.ac.uk/~zerbino/velvet/ + This installs the velvet assembler version 1.2.10 and contributed scripts including VelvetOptimiser.pl + </readme> + </package> +</tool_dependency>