annotate package/tool_dependencies.xml @ 2:3bc83ccf41a4 draft

Uploaded
author malbuquerque
date Tue, 20 Jan 2015 14:44:51 -0500
parents 5f241f2398c3
children b833f6538a4c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
1 <?xml version="1.0"?>
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
2 <tool_dependency>
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
3
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
4 <package name="boost" version="1.53">
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
5 <repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
6 </package>
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
7
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
8 <package name="bamtools" version="2.3.0">
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
9 <repository changeset_revision="ad46b5210186" name="package_bamtools_2_3_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu" />
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
10 </package>
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
11
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
12 <package name="seqtk" version="1.0.0">
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
13 <repository changeset_revision="35f0f4568ded" name="package_seqtk_1_0_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu" />
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
14 </package>
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
15
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
16 <package name="delly" version="0.6.1">
1
5f241f2398c3 Uploaded
malbuquerque
parents: 0
diff changeset
17 <install version="1.0">
0
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
18 <actions>
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
19 <action type="download_by_url">https://github.com/tobiasrausch/delly/archive/v0.6.1.tar.gz</action>
2
3bc83ccf41a4 Uploaded
malbuquerque
parents: 1
diff changeset
20 <action type="download_by_url">https://github.com/morinlab/galaxy_tools.git</action>
3bc83ccf41a4 Uploaded
malbuquerque
parents: 1
diff changeset
21 <action type="move_directory_files">
3bc83ccf41a4 Uploaded
malbuquerque
parents: 1
diff changeset
22 <source_directory>./galaxy_tools/delly/Makefile</source_directory>
3bc83ccf41a4 Uploaded
malbuquerque
parents: 1
diff changeset
23 <destination_directory>.</destination_directory>
3bc83ccf41a4 Uploaded
malbuquerque
parents: 1
diff changeset
24 </action>
0
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
25 <action type="shell_command">make all BOOST_ROOT=\$BOOST_ROOT BAMTOOLS_ROOT=\$BAMTOOLS_ROOT SEQTK_ROOT=\$SEQTK_ROOT</action>
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
26 <action type="move_directory_files">
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
27 <source_directory>.</source_directory>
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
28 <destination_directory>$INSTALL_DIR</destination_directory>
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
29 </action>
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
30 <action type="set_environment">
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
31 <environment_variable action="set_to" name="DELLY_DIR">$INSTALL_DIR</environment_variable>
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
32 </action>
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
33 </actions>
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
34 </install>
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
35 </package>
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
36
ace1798624b4 Uploaded
malbuquerque
parents:
diff changeset
37 </tool_dependency>