|
15
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
|
3 <set_environment version="1.0">
|
|
|
4 <environment_variable action="set_to" name="GATK2_PATH">/please set the path to your GATK2 dir in the corresponding env.sh file/</environment_variable>
|
|
|
5 </set_environment>
|
|
|
6 <!--
|
|
|
7 Use GATK2_SITE_OPTIONS to set additional parameters that should be inserted in every GATK2 call.
|
|
|
8 The intended use case was to prohibit GATK2 to collect and send data.
|
|
|
9 For example:
|
|
|
10
|
|
|
11 -et "NO_ET" -K "/data/gatk2_key_file" ##ET no phone home
|
|
|
12 -->
|
|
|
13 <set_environment version="1.0">
|
|
|
14 <environment_variable action="set_to" name="GATK2_SITE_OPTIONS"> </environment_variable>
|
|
|
15 </set_environment>
|
|
|
16
|
|
|
17 <package name="samtools" version="0.1.19">
|
|
|
18 <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
|
|
|
19 </package>
|
|
|
20 <package name="picard" version="1.56.0">
|
|
|
21 <repository changeset_revision="99a28567c3a3" name="package_picard_1_56_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
|
|
|
22 </package>
|
|
|
23 <package name="ggplot2" version="0.9.3">
|
|
|
24 <repository changeset_revision="07de191649b4" name="package_r_ggplot2_0_9_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
|
|
|
25 </package>
|
|
|
26 </tool_dependency>
|
