|
0
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
|
3
|
|
|
4 <package name="cmake" version="3.1.0">
|
|
5
|
5 <repository changeset_revision="a18ccb33a785" name="package_cmake_3_1_0" owner="malbuquerque" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
|
|
0
|
6 </package>
|
|
|
7
|
|
|
8 <package name="samtools" version="0.1.18">
|
|
5
|
9 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
|
|
0
|
10 </package>
|
|
|
11
|
|
|
12 <package name="bamtools" version="2.3.0">
|
|
|
13 <install version="1.0">
|
|
|
14 <actions>
|
|
|
15
|
|
6
|
16 <action type="set_environment_for_install">
|
|
|
17 <repository changeset_revision="a18ccb33a785" name="package_cmake_3_1_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu">
|
|
|
18 <package name="cmake" version="3.1.0" />
|
|
|
19 </repository>
|
|
|
20 </action>
|
|
|
21
|
|
|
22 <action type="set_environment_for_install">
|
|
|
23 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu">
|
|
|
24 <package name="samtools" version="3.1.0" />
|
|
|
25 </repository>
|
|
|
26 </action>
|
|
|
27
|
|
0
|
28 <action type="download_by_url">https://github.com/pezmaster31/bamtools/archive/v2.3.0.tar.gz</action>
|
|
|
29 <action type="shell_command">mkdir build</action>
|
|
3
|
30 <action type="change_directory">build</action>
|
|
|
31 <action type="shell_command">cmake ..</action>
|
|
0
|
32 <action type="shell_command">make</action>
|
|
4
|
33 <action type="change_directory">..</action>
|
|
0
|
34
|
|
|
35 <action type="move_directory_files">
|
|
|
36 <source_directory>./</source_directory>
|
|
|
37 <destination_directory>$INSTALL_DIR</destination_directory>
|
|
|
38 </action>
|
|
|
39
|
|
|
40 <action type="set_environment">
|
|
|
41 <environment_variable action="set_to" name="BAMTOOLS_ROOT">$INSTALL_DIR</environment_variable>
|
|
|
42 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
|
|
|
43 </action>
|
|
|
44
|
|
|
45 </actions>
|
|
|
46 </install>
|
|
|
47 </package>
|
|
|
48
|
|
|
49 </tool_dependency>
|
