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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 && cd samtools-parallel-mpileup && cd $(ls |grep samtools-) && make && cp samtools ../samtools-parallel-mpileup</action>
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8 <action type="move_file">
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9 <source>samtools-parallel-mpileup</source>
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10 <destination>$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 <package name="samtools" version="0.1.19">
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24 <install version="1.0">
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25 <actions_group>
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26 <actions os="linux" architecture="x86_64">
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27 <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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28 <action type="move_directory_files">
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29 <source_directory>.</source_directory>
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30 <destination_directory>$INSTALL_DIR</destination_directory>
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31 </action>
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32 </actions>
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33 <actions os="darwin" architecture="x86_64">
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34 <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.19-Darwin-x86_64.tgz</action>
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35 <action type="move_directory_files">
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36 <source_directory>.</source_directory>
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37 <destination_directory>$INSTALL_DIR</destination_directory>
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38 </action>
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39 </actions>
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40 <actions>
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41 <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2</action>
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42 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
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43 <action type="shell_command">make</action>
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44 <action type="move_file">
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45 <source>samtools</source>
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46 <destination>$INSTALL_DIR/bin</destination>
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47 </action>
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48 <action type="move_file">
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49 <source>bcftools/bcftools</source>
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50 <destination>$INSTALL_DIR/bin</destination>
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51 </action>
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52 <action type="move_file">
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53 <source>bcftools/vcfutils.pl</source>
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54 <destination>$INSTALL_DIR/bin</destination>
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55 </action>
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56 <action type="move_file">
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57 <source>libbam.a</source>
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58 <destination>$INSTALL_DIR/lib</destination>
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59 </action>
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60 <action type="move_directory_files">
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61 <source_directory>.</source_directory>
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62 <destination_directory>$INSTALL_DIR/include/bam</destination_directory>
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63 </action>
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64 </actions>
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65 <action type="set_environment">
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66 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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67 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
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68 <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
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69 </action>
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70 </actions_group>
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71 </install>
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72 <readme>
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73 Program: samtools (Tools for alignments in the SAM format)
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74 Version: 0.1.19-44428cd
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75
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76 Usage: samtools <command> [options]
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77
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78 Command: view SAM<->BAM conversion
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79 sort sort alignment file
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80 mpileup multi-way pileup
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81 depth compute the depth
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82 faidx index/extract FASTA
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83 tview text alignment viewer
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84 index index alignment
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85 idxstats BAM index stats (r595 or later)
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86 fixmate fix mate information
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87 flagstat simple stats
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88 calmd recalculate MD/NM tags and '=' bases
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89 merge merge sorted alignments
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90 rmdup remove PCR duplicates
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91 reheader replace BAM header
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92 cat concatenate BAMs
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93 bedcov read depth per BED region
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94 targetcut cut fosmid regions (for fosmid pool only)
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95 phase phase heterozygotes
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96 bamshuf shuffle and group alignments by name
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97 </readme>
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98 </package>
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99 <package name="VarScan" version="2.3.6">
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100 <install version="1.0">
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101 <actions>
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102 <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action>
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103 <action type="move_file">
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104 <source>VarScan.v2.3.6.jar</source>
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105 <destination>$INSTALL_DIR/jars</destination>
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106 </action>
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107 <action type="set_environment">
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108 <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
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109 </action>
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110 </actions>
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111 </install>
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112 <readme>
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113 Downloads VarScan2.
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114 </readme>
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115 </package>
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116
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117 <package name="VarScan" version="2.3.6">
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118 <install version="1.0">
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119 <actions>
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120 <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action>
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121 <action type="move_file">
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122 <source>VarScan.v2.3.6.jar</source>
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123 <destination>$INSTALL_DIR/jars</destination>
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124 </action>
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125 <action type="set_environment">
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126 <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
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127 </action>
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128 </actions>
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129 </install>
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130 <readme>
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131 Downloads VarScan2.
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132 </readme>
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133 </package>
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134 </tool_dependency>
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135
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