annotate tool_dependencies.xml @ 1:9b8e2a158073 draft

Fix typo in unified_genotyper.xml, add dir path in tool_dependencies.xml
author Jim Johnson <jj@umn.edu>
date Thu, 01 Nov 2012 13:44:41 -0500
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children a65944bad5c1
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="gatk" version="2.2">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-latest.tar.bz2</action>
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7 <!-- this expands into GenomeAnalysisTKLite-2.2-2-gd3f5a5e/
9b8e2a158073 Fix typo in unified_genotyper.xml, add dir path in tool_dependencies.xml
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8 which common_util.py tar_extraction_directory() does not find
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9 so the move file must contain the GenomeAnalysisTKLite-2.2-2-gd3f5a5e dir path
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10 -->
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11 <action type="move_file">
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12 <source>GenomeAnalysisTKLite-2.2-2-gd3f5a5e/GenomeAnalysisTKLite.jar</source>
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13 <destination>$INSTALL_DIR/GenomeAnalysisTK.jar</destination>
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14 </action>
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15 <action type="set_environment">
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16 <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable>
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17 </action>
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18 <action type="set_environment">
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19 <environment_variable name="GATK2_SITE_OPTIONS" action="set_to">--num_threads 4 --num_cpu_threads_per_data_thread 3 --phone_home STANDARD</environment_variable>
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20 </action>
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21 </actions>
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22 </install>
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23 <readme>
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24 The following GATK2 analysis types require a License for commercial use and the full GATK2 build will need to be manually installed:
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25
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26 haplotypecaller
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27 HaplotypeCaller Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an
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28 active region.
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29 HaplotypeResolver Haplotype-based resolution of variants in 2 different eval files.
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30
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31 reducereads
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32 CompareBAM Given two BAMs with different read groups, it compares them based on ReduceReads
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33 metrics.
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34 ReduceReads Reduces the BAM file using read based compression that keeps only essential information
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35 for variant calling
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36
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37
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38 See: http://www.appistry.com/gatk/gatk-faqs-static for Licensing details.
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39 The full GATK build can be acquired from: http://www.broadinstitute.org/gatk/download
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40 and GenomeAnalysisTK.jar need to be manually installed into the GATK2_PATH set for the GenomeAnalysisTKLite.jar
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41
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42 The GATK2_SITE_OPTIONS environment variable can be modified in the env.sh in the tool_dependencies path can be modified
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43 for the local installation.
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44
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45 </readme>
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46 </package>
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47 <package name="samtools" version="0.1.18">
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48 <install version="1.0">
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49 <actions>
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50 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
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51 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
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52 <action type="shell_command">make</action>
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53 <action type="move_file">
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54 <source>samtools</source>
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55 <destination>$INSTALL_DIR/bin</destination>
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56 </action>
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57 <action type="move_file">
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58 <source>misc/maq2sam-long</source>
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59 <destination>$INSTALL_DIR/bin</destination>
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60 </action>
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61 <action type="set_environment">
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62 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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63 </action>
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64 </actions>
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65 </install>
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66 <readme>
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67 Compiling SAMtools requires the ncurses and zlib development libraries.
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68 </readme>
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69 </package>
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70 </tool_dependency>