Mercurial > repos > malbuquerque > delly

comparison tool_dependencies.xml @ 37:941f4ecc5e88 draft

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author malbuquerque
date Tue, 20 Jan 2015 19:30:27 -0500
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36:cd89f768c05d 37:941f4ecc5e88
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 <action type="set_environment_for_install">
25 <repository changeset_revision="ad46b5210186" name="package_bamtools_2_3_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu">
26 <package name="bamtools" version="2.3.0" />
27 </repository>
28 </action>
29 <action type="set_environment_for_install">
30 <repository changeset_revision="35f0f4568ded" name="package_seqtk_1_0_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu">
31 <package name="seqtk" version="1.0.0" />
32 </repository>
33 </action>
34 <action type="download_by_url">https://github.com/tobiasrausch/delly/archive/v0.6.1.tar.gz</action>
35 <action type="shell_command">sleep 25</action>
36 <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>
37 <action type="move_directory_files">
38 <source_directory>.</source_directory>
39 <destination_directory>$INSTALL_DIR</destination_directory>
40 </action>
41 <action type="set_environment">
42 <environment_variable action="set_to" name="DELLY_DIR">$INSTALL_DIR</environment_variable>
43 </action>
44 </actions>
45 </install>
46 </package>
47
48 </tool_dependency>