Mercurial > repos > saskia-hiltemann > cgatools_v17

comparison tool_dependencies.xml @ 1:3a2e0f376f26 draft

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Minor change to tv2vcf.xml to allow for workflow automation
author dgdekoning
date Wed, 21 Oct 2015 10:09:15 -0400
parents
children 977861cbcf10
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0:751b62d30ae1 1:3a2e0f376f26
1 <?xml version="1.0"?>
2 <tool_dependency>
3
4 <package name="cgatools17" version="1">
5 <install version="1.0">
6 <actions>
7 <action type="download_by_url">http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz</action>
8 <action type="shell_command"> chmod a+x bin/cgatools</action>
9 <action type="move_file">
10 <source>bin/cgatools</source>
11 <destination>$INSTALL_DIR/bin</destination>
12 </action>
13 <action type="set_environment">
14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
15 <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
16 </action>
17 </actions>
18 </install>
19 <readme>
20 Downloads and installs the cgatools binary.
21 </readme>
22 </package>
23
24 <package name="vcf_to_listVariants" version="1.0.0">
25 <install version="1.0">
26 <actions>
27 <!--
28 <action type="move_file">
29 <source>$REPOSITORY_INSTALL_DIR/cgatools_v17/bin/vcf_to_listVariants.py</source>
30 <destination>$INSTALL_DIR/bin/</destination>
31 </action>
32 -->
33
34 <action type="shell_command">cp $REPOSITORY_INSTALL_DIR/cgatools_v17/tools/cgatools17/vcf_to_listVariants.py $INSTALL_DIR</action>
35 <action type="chmod">
36 <file mode="755">$INSTALL_DIR/vcf_to_listVariants.py</file>
37 </action>
38
39 <action type="set_environment">
40 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
41 <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR/cgatools_v17/bin</environment_variable>
42 <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR/cgatools_v17</environment_variable>
43 <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR/bin</environment_variable>
44 </action>
45 </actions>
46 </install>
47 </package>
48
49 </tool_dependency>