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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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3
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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="9f412e12b103" name="package_samtools_0_1_19" owner="iuc" toolshed="http://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="http://testtoolshed.g2.bx.psu.edu" />
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22 </package>
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23
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24 <package name="gatk2_r_dependencies" version="2.8">
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25 <install version="1.0">
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26 <actions>
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27 <action type="setup_r_environment">
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28
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29 <repository changeset_revision="2c0a13200a73" name="package_r_2_11_0" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu">
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30 <package name="R" version="2.11.0" />
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31 </repository>
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32 <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/colorspace_1.2-4.tar.gz</package>
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33 <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/stringr_0.6.2.tar.gz</package>
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34 <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/RColorBrewer_1.0-5.tar.gz</package>
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35 <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/dichromat_2.0-0.tar.gz</package>
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36 <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/munsell_0.4.2.tar.gz</package>
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37 <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/labeling_0.2.tar.gz</package>
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38 <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/plyr_1.8.1.tar.gz</package>
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39 <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/digest_0.6.4.tar.gz</package>
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40 <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/gtable_0.1.2.tar.gz</package>
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41 <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/reshape2_1.2.2.tar.gz</package>
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42 <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/scales_0.2.3.tar.gz</package>
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43 <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/proto_0.3-10.tar.gz</package>
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44 <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/ggplot2_0.9.3.1.tar.gz</package>
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45 </action>
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46 </actions>
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47 </install>
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48 <readme>
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49 R depencies for GATK2.
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50 </readme>
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51 </package>
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52 </tool_dependency>
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