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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <set_environment version="1.0">
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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>
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5 </set_environment>
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6 <!--
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7 Use GATK2_SITE_OPTIONS to set additional parameters that should be inserted in every GATK2 call.
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8 The intended use case was to prohibit GATK2 to collect and send data.
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9 For example:
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10
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11 -et "NO_ET" -K "/data/gatk2_key_file" ##ET no phone home
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12 -->
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13 <set_environment version="1.0">
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14 <environment_variable action="set_to" name="GATK2_SITE_OPTIONS"> </environment_variable>
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15 </set_environment>
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16
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17 <package name="samtools" version="0.1.19">
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18 <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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19 </package>
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20 <package name="picard" version="1.56.0">
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21 <repository changeset_revision="7206dbf34dcd" name="package_picard_1_56_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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22 </package>
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23 <package name="ggplot2" version="0.9.3">
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24 <repository changeset_revision="ade406d47752" name="package_r_ggplot2_0_9_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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25 </package>
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26 </tool_dependency>
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