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>