Mercurial > repos > jjohnson > package_samtools_0_1_19

annotate tool_dependencies.xml @ 0:06697b4877f9 draft default tip

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author jjohnson
date Tue, 03 Sep 2013 11:48:30 -0400
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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>
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6 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
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7 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
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8 <action type="shell_command">make</action>
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9 <action type="shell_command">chmod ugo+rx misc/*.p?</action>
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10 <action type="shell_command">mkdir misc/bin</action>
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11 <action type="shell_command">cp -p `find misc -type f -perm -555` misc/bin/</action>
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12 <action type="move_file">
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13 <source>samtools</source>
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14 <destination>$INSTALL_DIR/bin</destination>
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15 </action>
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16 <action type="move_file">
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17 <source>bcftools/bcftools</source>
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18 <destination>$INSTALL_DIR/bin</destination>
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19 </action>
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20 <action type="move_file">
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21 <source>bcftools/vcfutils.pl</source>
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22 <destination>$INSTALL_DIR/bin</destination>
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23 </action>
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24 <action type="move_directory_files">
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25 <source_directory>misc/bin</source_directory>
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26 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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27 </action>
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28 <action type="set_environment">
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29 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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30 </action>
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31 </actions>
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32 </install>
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33 <readme>
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34 Program: samtools (Tools for alignments in the SAM format)
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35 Version: 0.1.19
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36
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37 Usage: samtools &lt;command&gt; [options]
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38
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39 Command: view SAM&lt;-&gt;BAM conversion
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40 sort sort alignment file
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41 mpileup multi-way pileup
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42 depth compute the depth
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43 faidx index/extract FASTA
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44 tview text alignment viewer
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45 index index alignment
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46 idxstats BAM index stats (r595 or later)
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47 fixmate fix mate information
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48 flagstat simple stats
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49 calmd recalculate MD/NM tags and '=' bases
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50 merge merge sorted alignments
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51 rmdup remove PCR duplicates
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52 reheader replace BAM header
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53 cat concatenate BAMs
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54 targetcut cut fosmid regions (for fosmid pool only)
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55 phase phase heterozygotes
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56
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57 This also installs bcftools and misc utility commands:
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58 bcftools
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59 vcfutils.pl
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60 ace2sam
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61 bamcheck
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62 blast2sam.pl
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63 bowtie2sam.pl
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64 export2sam.pl
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65 interpolate_sam.pl
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66 maq2sam-long
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67 maq2sam-short
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68 md5fa
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69 md5sum-lite
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70 novo2sam.pl
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71 psl2sam.pl
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72 sam2vcf.pl
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73 samtools.pl
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74 soap2sam.pl
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75 varfilter.py
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76 wgsim
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77 wgsim_eval.pl
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78 zoom2sam.pl
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79 </readme>
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80 </package>
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81 </tool_dependency>