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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="0.1.19">
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4 <install version="1.0">
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5 <actions_group>
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6 <actions os="linux" architecture="x86_64">
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7 <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.19-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>$INSTALL_DIR</destination_directory>
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11 </action>
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12 </actions>
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13 <actions os="darwin" architecture="x86_64">
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14 <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.19-Darwin-x86_64.tgz</action>
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15 <action type="move_directory_files">
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16 <source_directory>.</source_directory>
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17 <destination_directory>$INSTALL_DIR</destination_directory>
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18 </action>
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19 </actions>
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20 <actions>
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21 <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2</action>
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22 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
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23 <action type="shell_command">make</action>
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24 <action type="move_file">
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25 <source>samtools</source>
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26 <destination>$INSTALL_DIR/bin</destination>
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27 </action>
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28 <action type="move_file">
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29 <source>bcftools/bcftools</source>
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30 <destination>$INSTALL_DIR/bin</destination>
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31 </action>
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32 <action type="move_file">
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33 <source>bcftools/vcfutils.pl</source>
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34 <destination>$INSTALL_DIR/bin</destination>
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35 </action>
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36 <action type="move_file">
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37 <source>libbam.a</source>
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38 <destination>$INSTALL_DIR/lib</destination>
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39 </action>
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40 <action type="move_directory_files">
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41 <source_directory>.</source_directory>
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42 <destination_directory>$INSTALL_DIR/include/bam</destination_directory>
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43 </action>
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44 </actions>
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45 <action type="set_environment">
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46 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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47 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
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48 <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
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49 </action>
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50 </actions_group>
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51 </install>
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52 <readme>
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53 Program: samtools (Tools for alignments in the SAM format)
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54 Version: 0.1.19-44428cd
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55
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56 Usage: samtools <command> [options]
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57
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58 Command: view SAM<->BAM conversion
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59 sort sort alignment file
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60 mpileup multi-way pileup
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61 depth compute the depth
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62 faidx index/extract FASTA
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63 tview text alignment viewer
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64 index index alignment
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65 idxstats BAM index stats (r595 or later)
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66 fixmate fix mate information
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67 flagstat simple stats
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68 calmd recalculate MD/NM tags and '=' bases
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69 merge merge sorted alignments
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70 rmdup remove PCR duplicates
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71 reheader replace BAM header
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72 cat concatenate BAMs
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73 bedcov read depth per BED region
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74 targetcut cut fosmid regions (for fosmid pool only)
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75 phase phase heterozygotes
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76 bamshuf shuffle and group alignments by name
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77 </readme>
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78 </package>
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79 </tool_dependency>
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