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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="samtools" version="1.2">
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4 <install version="1.0">
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5 <actions_group>
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6 <actions architecture="x86_64" os="linux">
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7 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz</action>
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8 <action type="move_directory_files">
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9 <source_directory>.</source_directory>
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10 <destination_directory>$INSTALL_DIR</destination_directory>
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11 </action>
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12 </actions>
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13 <actions>
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14 <package name="ncurses" version="5.9">
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15 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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16 </package>
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17 <package name="zlib" version="1.2.8">
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18 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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19 </package>
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20 <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action>
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21 <action type="set_environment_for_install">
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22 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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23 <package name="ncurses" version="5.9" />
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24 </repository>
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25 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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26 <package name="zlib" version="1.2.8" />
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27 </repository>
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28 </action>
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29 <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action>
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30 <action type="shell_command">sed -i -e 's/-lcurses/-lncurses/' Makefile</action>
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31 <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action>
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32 <action type="shell_command">make</action>
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33 <action type="move_file">
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34 <source>samtools</source>
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35 <destination>$INSTALL_DIR/bin</destination>
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36 </action>
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37 </actions>
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38 <action type="set_environment">
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39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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40 <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
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41 </action>
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42 </actions_group>
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43 </install>
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44 <readme>
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45 Program: samtools (Tools for alignments in the SAM format)
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46 Version: 1.2
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47
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48 Usage: samtools <command> [options]
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49
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50 Commands:
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51 -- indexing
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52 faidx index/extract FASTA
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53 index index alignment
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54 -- editing
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55 calmd recalculate MD/NM tags and '=' bases
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56 fixmate fix mate information
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57 reheader replace BAM header
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58 rmdup remove PCR duplicates
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59 targetcut cut fosmid regions (for fosmid pool only)
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60 -- file operations
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61 bamshuf shuffle and group alignments by name
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62 cat concatenate BAMs
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63 merge merge sorted alignments
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64 mpileup multi-way pileup
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65 sort sort alignment file
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66 split splits a file by read group
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67 bam2fq converts a BAM to a FASTQ
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68 -- stats
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69 bedcov read depth per BED region
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70 depth compute the depth
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71 flagstat simple stats
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72 idxstats BAM index stats
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73 phase phase heterozygotes
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74 stats generate stats (former bamcheck)
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75 -- viewing
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76 flags explain BAM flags
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77 tview text alignment viewer
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78 view SAM<->BAM<->CRAM conversion
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79 </readme>
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80 </package>
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81 </tool_dependency>
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