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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 <action type="move_file">
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8 <source>GenomeAnalysisTKLite.jar</source>
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9 <destination>$INSTALL_DIR/GenomeAnalysisTK.jar</destination>
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10 </action>
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11 <action type="set_environment">
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12 <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable>
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13 </action>
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14 <action type="set_environment">
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15 <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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16 </action>
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17 </actions>
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18 </install>
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19 <readme>
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20 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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21
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22 haplotypecaller
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23 HaplotypeCaller Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an
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24 active region.
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25 HaplotypeResolver Haplotype-based resolution of variants in 2 different eval files.
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26
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27 reducereads
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28 CompareBAM Given two BAMs with different read groups, it compares them based on ReduceReads
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29 metrics.
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30 ReduceReads Reduces the BAM file using read based compression that keeps only essential information
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31 for variant calling
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32
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33
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34 See: http://www.appistry.com/gatk/gatk-faqs-static for Licensing details.
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35 The full GATK build can be acquired from: http://www.broadinstitute.org/gatk/download
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36 and GenomeAnalysisTK.jar need to be manually installed into the GATK2_PATH set for the GenomeAnalysisTKLite.jar
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37
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38 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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39 for the local installation.
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40
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41 </readme>
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42 </package>
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43 <package name="samtools" version="0.1.18">
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44 <install version="1.0">
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45 <actions>
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46 <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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47 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
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48 <action type="shell_command">make</action>
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49 <action type="move_file">
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50 <source>samtools</source>
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51 <destination>$INSTALL_DIR/bin</destination>
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52 </action>
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53 <action type="move_file">
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54 <source>misc/maq2sam-long</source>
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55 <destination>$INSTALL_DIR/bin</destination>
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56 </action>
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57 <action type="set_environment">
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58 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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59 </action>
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60 </actions>
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61 </install>
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62 <readme>
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63 Compiling SAMtools requires the ncurses and zlib development libraries.
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64 </readme>
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65 </package>
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66 </tool_dependency>
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