Mercurial > repos > jeremie > package_breakdancer_1_4_4
changeset 0:291c03afa791 draft
Uploaded
| author | jeremie |
|---|---|
| date | Wed, 02 Jul 2014 09:45:29 -0400 |
| parents | |
| children | 96b118fc9c37 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 26 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jul 02 09:45:29 2014 -0400 @@ -0,0 +1,26 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="breakdancer" version="1.4.4"> + <install version="1.0"> + <actions_group> + <actions> + <action type="shell_command">git clone --recursive https://github.com/genome/breakdancer</action> + <!-- <action type="shell_command">git checkout tags/v1.4.4</action> --> + <action type="shell_command">mkdir build</action> + <action type="change_directory">build</action> + <action type="shell_command">cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local</action> + <action type="shell_command">make</action> + <action type="move_file"><source>bin/breakdancer-max</source><destination>$INSTALL_DIR/bin</destination></action> + <action type="move_file"><source>../perl/bam2cfg.pl</source><destination>$INSTALL_DIR/bin</destination></action> + <action type="move_file"><source>../perl/AlnParser.pm</source><destination>$INSTALL_DIR/bin</destination></action> + <action type="shell_command">wget https://raw.githubusercontent.com/ALLBio/allbiotc2/master/breakdancer/breakdancer2vcf.py</action> + <action type="move_file"><source>breakdancer2vcf.py</source><destination>$INSTALL_DIR/bin</destination></action> + <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> + <action type="set_environment"><environment_variable name="BREAKDANCER_BIN" action="set_to">$INSTALL_DIR/bin</environment_variable></action> + </actions> + </actions_group> + </install> + <readme> + </readme> + </package> +</tool_dependency> \ No newline at end of file