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Commit message:
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tool_dependencies.xml |
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| diff -r 000000000000 -r 1fde0b7d7d40 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Sep 24 11:57:36 2015 -0400 |
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| @@ -0,0 +1,137 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="idba" version="1.0"> + <install version="1.0"> + <actions> + <action type="shell_command">git clone https://github.com/loneknightpy/idba.git idba</action> + <action type="change_directory">idba</action> + <action type="shell_command">./build.sh</action> + <action type="shell_command">./configure</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>bin/fa2fq</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/filter_blat</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/filter_contigs</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/filterfa</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/fq2fa</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/idba</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/idba_hybrid</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/idba_tran</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/idba_tran_test</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/idba_ud</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/parallel_blat</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/parallel_rna_blat</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/print_graph</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/raw_n50</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/sample_reads</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/scaffold</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/shuffle_reads</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/sim_reads</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/sim_reads_tran</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/sort_psl</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/sort_reads</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/split_fa</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/split_fq</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/split_scaffold</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/test</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/validate_component</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/validate_contigs_blat</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/validate_contigs_mummer</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/validate_reads_blat</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bin/validate_rna</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + </package> +</tool_dependency> |