Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam

annotate tool_dependencies.xml @ 52:b2dc8ab51a79 draft

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author yhoogstrate
date Wed, 05 Mar 2014 09:18:21 -0500
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <!-- Optimized samtools (for threaded mpileup) -->
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4 <package name="samtools-parallel-mpileup" version="0.1.19">
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5 <install version="1.0">
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6 <actions>
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7 <action type="shell_command">svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup &amp;&amp; cd samtools-parallel-mpileup &amp;&amp; cd $(ls |grep samtools-) &amp;&amp; make &amp;&amp; cp samtools ../samtools-parallel-mpileup</action>
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8 <action type="move_file">
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9 <source>samtools-parallel-mpileup</source>
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10 <destination>$INSTALL_DIR/bin</destination>
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11 </action>
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12 <action type="set_environment">
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13 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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14 <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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15 </action>
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16 </actions>
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17 </install>
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18 <readme>
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19 Downloads and installs a modified version of samtools, able to paralellize the mpileup function.
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20 </readme>
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21 </package>
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22
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23 <!-- Classical samtools (doesn't support threaded mpileup) -->
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24 <package name="samtools" version="0.1.19">
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25 <install version="1.0">
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26 <actions>
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27 <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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28 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
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29 <action type="shell_command">make</action>
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30 <action type="shell_command">chmod ugo+rx misc/*.p?</action>
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31 <action type="shell_command">mkdir misc/bin</action>
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32 <action type="shell_command">cp -p `find misc -type f -perm -555` misc/bin/</action>
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33 <action type="move_file">
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34 <source>samtools</source>
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35 <destination>$INSTALL_DIR/bin</destination>
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36 </action>
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37 <action type="move_file">
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38 <source>bcftools/bcftools</source>
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39 <destination>$INSTALL_DIR/bin</destination>
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40 </action>
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41 <action type="move_file">
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42 <source>bcftools/vcfutils.pl</source>
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43 <destination>$INSTALL_DIR/bin</destination>
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44 </action>
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45 <action type="move_directory_files">
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46 <source_directory>misc/bin</source_directory>
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47 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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48 </action>
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49 <action type="set_environment">
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50 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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51 </action>
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52 </actions>
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53 </install>
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54 <readme>
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55 Program: samtools (Tools for alignments in the SAM format)
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56 Version: 0.1.19
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57
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58 Usage: samtools &lt;command&gt; [options]
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59
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60 Command: view SAM&lt;-&gt;BAM conversion
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61 sort sort alignment file
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62 mpileup multi-way pileup
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63 depth compute the depth
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64 faidx index/extract FASTA
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65 tview text alignment viewer
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66 index index alignment
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67 idxstats BAM index stats (r595 or later)
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68 fixmate fix mate information
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69 flagstat simple stats
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70 calmd recalculate MD/NM tags and '=' bases
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71 merge merge sorted alignments
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72 rmdup remove PCR duplicates
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73 reheader replace BAM header
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74 cat concatenate BAMs
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75 targetcut cut fosmid regions (for fosmid pool only)
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76 phase phase heterozygotes
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77
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78 This also installs bcftools and misc utility commands:
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79 bcftools
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80 vcfutils.pl
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81 ace2sam
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82 bamcheck
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83 blast2sam.pl
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84 bowtie2sam.pl
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85 export2sam.pl
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86 interpolate_sam.pl
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87 maq2sam-long
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88 maq2sam-short
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89 md5fa
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90 md5sum-lite
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91 novo2sam.pl
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92 psl2sam.pl
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93 sam2vcf.pl
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94 samtools.pl
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95 soap2sam.pl
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96 varfilter.py
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97 wgsim
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98 wgsim_eval.pl
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99 zoom2sam.pl
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100 </readme>
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101 </package>
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102
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103 <package name="VarScan" version="2.3.6">
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104 <install version="1.0">
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105 <actions>
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106 <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action>
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107 <action type="move_file">
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108 <source>VarScan.v2.3.6.jar</source>
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109 <destination>$INSTALL_DIR/jars</destination>
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110 </action>
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111 <action type="set_environment">
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112 <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
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113 </action>
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114 </actions>
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115 </install>
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116 <readme>
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117 Downloads VarScan2.
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118 </readme>
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119 </package>
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120 </tool_dependency>