Mercurial > repos > jjohnson > snpeff_with_dep

annotate tool_dependencies.xml @ 10:9cd24981dbd2

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
tool_dependencies.xml - add unzip shell_command
author Jim Johnson <jj@umn.edu>
date Tue, 18 Sep 2012 08:36:28 -0500
parents 38b3a6b97bd1
children e9e4ff80e72b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
388f178f9e13 Uploaded
jjohnson
parents:
diff changeset
1 <?xml version="1.0"?>
388f178f9e13 Uploaded
jjohnson
parents:
diff changeset
2 <tool_dependency>
388f178f9e13 Uploaded
jjohnson
parents:
diff changeset
3 <set_environment version="1.0">
4
ceaa79a5ee16 Actions for tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
4 <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
0
388f178f9e13 Uploaded
jjohnson
parents:
diff changeset
5 </set_environment>
388f178f9e13 Uploaded
jjohnson
parents:
diff changeset
6 <package name="snpEff" version="3.0f">
388f178f9e13 Uploaded
jjohnson
parents:
diff changeset
7 <install version="1.0">
388f178f9e13 Uploaded
jjohnson
parents:
diff changeset
8 <actions>
7
3cb1d19d57d1 Remove download at end of url
Jim Johnson <jj@umn.edu>
parents: 6
diff changeset
9 <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip</action>
10
9cd24981dbd2 tool_dependencies.xml - add unzip shell_command
Jim Johnson <jj@umn.edu>
parents: 9
diff changeset
10 <action type="shell_command">unzip snpEff_latest_core.zip</action>
4
ceaa79a5ee16 Actions for tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
11 <action type="move_file">
9
38b3a6b97bd1 Add src dir snpEff_3_0 to move_file in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 8
diff changeset
12 <source>snpEff_3_0/SnpSift.jar</source>
4
ceaa79a5ee16 Actions for tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
13 <destination>$INSTALL_DIR/bin</destination>
ceaa79a5ee16 Actions for tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
14 </action>
ceaa79a5ee16 Actions for tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
15 <action type="move_file">
9
38b3a6b97bd1 Add src dir snpEff_3_0 to move_file in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 8
diff changeset
16 <source>snpEff_3_0/snpEff.jar</source>
38b3a6b97bd1 Add src dir snpEff_3_0 to move_file in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 8
diff changeset
17 <destination>$INSTALL_DIR/bin</destination>
38b3a6b97bd1 Add src dir snpEff_3_0 to move_file in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 8
diff changeset
18 </action>
38b3a6b97bd1 Add src dir snpEff_3_0 to move_file in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 8
diff changeset
19 <action type="move_file">
38b3a6b97bd1 Add src dir snpEff_3_0 to move_file in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 8
diff changeset
20 <source>snpEff_3_0/snpEff.config</source>
4
ceaa79a5ee16 Actions for tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
21 <destination>$INSTALL_DIR/bin</destination>
ceaa79a5ee16 Actions for tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
22 </action>
ceaa79a5ee16 Actions for tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
23 <action type="move_directory_files">
9
38b3a6b97bd1 Add src dir snpEff_3_0 to move_file in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 8
diff changeset
24 <source_directory>snpEff_3_0/scripts</source_directory>
4
ceaa79a5ee16 Actions for tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
25 <destination_directory>$INSTALL_DIR/bin</destination_directory>
ceaa79a5ee16 Actions for tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
26 </action>
ceaa79a5ee16 Actions for tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
27 <action type="set_environment">
6
e6b662b96061 Fix typo in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
28 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
4
ceaa79a5ee16 Actions for tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
29 </action>
0
388f178f9e13 Uploaded
jjohnson
parents:
diff changeset
30 </actions>
388f178f9e13 Uploaded
jjohnson
parents:
diff changeset
31 </install>
388f178f9e13 Uploaded
jjohnson
parents:
diff changeset
32 <readme>
388f178f9e13 Uploaded
jjohnson
parents:
diff changeset
33 </readme>
388f178f9e13 Uploaded
jjohnson
parents:
diff changeset
34 </package>
388f178f9e13 Uploaded
jjohnson
parents:
diff changeset
35
388f178f9e13 Uploaded
jjohnson
parents:
diff changeset
36 </tool_dependency>
388f178f9e13 Uploaded
jjohnson
parents:
diff changeset
37