|
4
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
|
3 <set_environment version="1.0">
|
|
|
4 <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
|
|
|
5 </set_environment>
|
|
|
6 <package name="samtools" version="0.1.12">
|
|
|
7 <install version="1.0">
|
|
|
8 <actions>
|
|
5
|
9 <action type="shell_command">git clone https://github.com/modENCODE-DCC/Galaxy/blob/master/tool_shed_dependencies/bamedit/samtoolspkg.tar</action>
|
|
4
|
10 <action type="shell_command">chmod ago+x samtools</action>
|
|
|
11 <action type="shell_command">chmod ago+x maq2sam-long</action>
|
|
|
12 <action type="move_file">
|
|
|
13 <source>samtools</source>
|
|
|
14 <destination>$INSTALL_DIR/bin</destination>
|
|
|
15 </action>
|
|
|
16 <action type="move_file">
|
|
|
17 <source>maq2sam-long</source>
|
|
|
18 <destination>$INSTALL_DIR/bin</destination>
|
|
|
19 </action>
|
|
|
20 <action type="set_environment">
|
|
|
21 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
|
|
|
22 </action>
|
|
|
23 </actions>
|
|
|
24 </install>
|
|
|
25 <readme>Compiling SAMtools requires the ncurses and zlib development libraries.</readme>
|
|
|
26 </package>
|
|
|
27 </tool_dependency>
|
