Mercurial > repos > malbuquerque > delly

comparison tool_dependencies.xml @ 39:1e5b1f1b46c1 draft default tip

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author malbuquerque
date Tue, 20 Jan 2015 19:36:31 -0500
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38:a9a4557de9ca 39:1e5b1f1b46c1
1 <?xml version="1.0"?>
2 <tool_dependency>
3
4 <package name="boost" version="1.53.0">
5 <repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
6 </package>
7
8 <package name="bamtools" version="2.3.0">
9 <repository changeset_revision="ad46b5210186" name="package_bamtools_2_3_0" owner="malbuquerque" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
10 </package>
11
12 <package name="seqtk" version="1.0.0">
13 <repository changeset_revision="35f0f4568ded" name="package_seqtk_1_0_0" owner="malbuquerque" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
14 </package>
15
16 <package name="delly" version="0.6.1">
17 <install version="1.0">
18 <actions>
19 <action type="set_environment_for_install">
20 <repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
21 <package name="boost" version="1.53.0" />
22 </repository>
23 </action>
24
25 <action type="set_environment_for_install">
26 <repository changeset_revision="ad46b5210186" name="package_bamtools_2_3_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu">
27 <package name="bamtools" version="2.3.0" />
28 </repository>
29 </action>
30
31 <action type="set_environment_for_install">
32 <repository changeset_revision="35f0f4568ded" name="package_seqtk_1_0_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu">
33 <package name="seqtk" version="1.0.0" />
34 </repository>
35 </action>
36
37 <action type="download_by_url">https://github.com/tobiasrausch/delly/archive/v0.6.1.tar.gz</action>
38 <action type="shell_command">pwd &gt; ~/delly.pwd.txt</action>
39 <action type="shell_command">echo $INSTALL_DIR &gt; ~/delly.dir.txt</action>
40 <action type="shell_command">sleep 25</action>
41 <action type="shell_command">make -f $REPOSITORY_INSTALL_DIR/Makefile all BOOST_ROOT=$BOOST_ROOT_DIR/ BAMTOOLS_ROOT=$BAMTOOLS_ROOT/ SEQTK_ROOT=$SEQTK_ROOT/</action>
42 <action type="move_directory_files">
43 <source_directory>.</source_directory>
44 <destination_directory>$INSTALL_DIR</destination_directory>
45 </action>
46 <action type="set_environment">
47 <environment_variable action="set_to" name="DELLY_DIR">$INSTALL_DIR</environment_variable>
48 </action>
49 </actions>
50 </install>
51 </package>
52
53 </tool_dependency>