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0
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="blast+" version="2.2.28">
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26
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4 <repository changeset_revision="6f6a8be93479" name="package_blast_plus_2_2_28" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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0
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5 </package>
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6 <package name="hmmer" version="3.0">
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26
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7 <repository changeset_revision="a44693e3a2c4" name="package_hmmer_3_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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0
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8 </package>
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9 <package name="muscle" version="3.8.31">
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26
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10 <repository changeset_revision="a8912a41ecc8" name="package_muscle_3_8_31" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5
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11 </package>
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18
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12 <package name="biopython" version="1.62">
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26
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13 <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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18
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14 </package>
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15
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17
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16 <package name="helperlibs" version="0.1.2">
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7
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17 <install version="1.0">
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5
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18 <actions>
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17
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19 <action type="download_by_url">https://pypi.python.org/packages/source/h/helperlibs/helperlibs-0.1.2.tar.gz</action>
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20 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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25
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21 <action type="shell_command">
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22 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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23 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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24 </action>
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17
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25 <action type="set_environment">
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26 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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27 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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28 </action>
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5
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29 </actions>
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30 </install>
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31 <readme>
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17
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32 helperlibs python library
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33 </readme>
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34 </package>
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18
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35
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21
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36 <package name="cssselect" version="0.9">
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37 <install version="1.0">
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38 <actions>
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39 <action type="download_by_url">https://pypi.python.org/packages/source/c/cssselect/cssselect-0.9.tar.gz</action>
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40 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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25
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41 <action type="shell_command">
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42 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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43 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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44 </action>
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21
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45 <action type="set_environment">
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46 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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47 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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48 </action>
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49 </actions>
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50 </install>
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51 <readme>
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52 cssselect python library
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53 </readme>
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54 </package>
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55
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18
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56 <package name="pyquery" version="1.2.6">
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57 <install version="1.0">
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58 <actions>
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20
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59 <action type="download_by_url">https://github.com/gawel/pyquery/archive/1.2.6.tar.gz</action>
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18
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60 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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25
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61 <action type="shell_command">
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62 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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63 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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64 </action>
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18
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65 <action type="set_environment">
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66 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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67 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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68 </action>
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69 </actions>
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70 </install>
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71 <readme>
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21
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72 pyquery python library
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18
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73 </readme>
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74 </package>
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75
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17
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76 <package name="straight.plugin" version="1.4.0-post-1">
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77 <install version="1.0">
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78 <actions>
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79 <action type="download_by_url">https://pypi.python.org/packages/source/s/straight.plugin/straight.plugin-1.4.0-post-1.tar.gz</action>
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80 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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25
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81 <action type="shell_command">
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82 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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83 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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84 </action>
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17
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85 <action type="set_environment">
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86 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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87 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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88 </action>
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89 </actions>
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90 </install>
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91 <readme>
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92 straight.plugin python library
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5
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93 </readme>
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0
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94 </package>
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95 <package name="antismash" version="2.0.2">
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96 <install version="1.0">
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97 <actions_group>
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25
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98 <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. -->
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8
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99 <actions architecture="x86_64" os="darwin">
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100 <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action>
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101 <action type="move_directory_files">
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102 <source_directory>.</source_directory>
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103 <destination_directory>$INSTALL_DIR</destination_directory>
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104 </action>
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105 <action type="chmod">
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106 <file mode="750">$INSTALL_DIR/run_antismash.py</file>
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107 </action>
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24
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108 <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and
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109 we need to copy this plugin into the correct location.
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110 -->
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111 <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action>
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112 <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action>
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113 <action type="move_file">
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114 <source>__init__.py</source>
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115 <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination>
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116 </action>
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117 <!-- AntiSmash has a prerequirement check that is not useful for us, because we
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118 do not offer the option for genprediction and do not install glimmer and Co.
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119 For that reason deactivate the check.
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120 -->
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121 <action type="shell_command">sed -i 's/check_prereqs(plugins, options) > 0/False/g' $INSTALL_DIR/run_antismash.py</action>
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122 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
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25
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123 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
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24
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124 </actions>
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125
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25
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126 <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. -->
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24
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127 <actions architecture="i386" os="darwin">
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128 <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action>
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129 <action type="move_directory_files">
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130 <source_directory>.</source_directory>
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131 <destination_directory>$INSTALL_DIR</destination_directory>
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132 </action>
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133 <action type="chmod">
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134 <file mode="750">$INSTALL_DIR/run_antismash.py</file>
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135 </action>
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136 <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and
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137 we need to copy this plugin into the correct location.
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138 -->
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139 <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action>
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140 <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action>
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141 <action type="move_file">
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142 <source>__init__.py</source>
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143 <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination>
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144 </action>
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145 <!-- AntiSmash has a prerequirement check that is not useful for us, because we
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146 do not offer the option for genprediction and do not install glimmer and Co.
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147 For that reason deactivate the check.
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148 -->
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17
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149 <action type="shell_command">sed -i 's/check_prereqs(plugins, options) > 0/False/g' $INSTALL_DIR/run_antismash.py</action>
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13
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150 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
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151 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
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8
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152 </actions>
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24
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153
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0
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154 <!-- Download the binaries for AntiSmash compatible with 64-bit Linux. -->
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6
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155 <actions architecture="x86_64" os="linux">
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7
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156 <action target_filename="antismash-2.0.2.tar.bz2" type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.x86_64.tar.bz2</action>
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12
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157 <action type="move_directory_files">
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158 <source_directory>.</source_directory>
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159 <destination_directory>$INSTALL_DIR</destination_directory>
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160 </action>
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0
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161 <action type="chmod">
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162 <file mode="750">$INSTALL_DIR/run_antismash.py</file>
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163 </action>
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23
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164 <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and
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165 we need to copy this plugin into the correct location.
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166 -->
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167 <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action>
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168 <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action>
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169 <action type="move_file">
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170 <source>__init__.py</source>
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171 <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination>
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172 </action>
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15
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173 <!-- AntiSmash has a prerequirement check that is not useful for us, because we
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174 do not offer the option for genprediction and do not install glimmer and Co.
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175 For that reason deactivate the check.
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176 -->
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17
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177 <action type="shell_command">sed -i 's/check_prereqs(plugins, options) > 0/False/g' $INSTALL_DIR/run_antismash.py</action>
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12
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178 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
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179 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
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0
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180 </actions>
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24
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181
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0
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182 <!-- Download the binaries for AntiSmash compatible with 32-bit Linux. -->
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6
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183 <actions architecture="i386" os="linux">
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0
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184 <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.i686.tar.bz2</action>
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185 <action type="move_directory_files">
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186 <source_directory>.</source_directory>
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187 <destination_directory>$INSTALL_DIR</destination_directory>
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188 </action>
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189 <action type="chmod">
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190 <file mode="750">$INSTALL_DIR/run_antismash.py</file>
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191 </action>
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24
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192 <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and
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193 we need to copy this plugin into the correct location.
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194 -->
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195 <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action>
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196 <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action>
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197 <action type="move_file">
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198 <source>__init__.py</source>
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199 <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination>
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200 </action>
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16
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201 <!-- AntiSmash has a prerequirement check that is not useful for us, because we
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202 do not offer the option for genprediction and do not install glimmer and Co.
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203 For that reason deactivate the check.
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204 -->
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17
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205 <action type="shell_command">sed -i 's/check_prereqs(plugins, options) > 0/False/g' $INSTALL_DIR/run_antismash.py</action>
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13
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206 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
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207 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
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3
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208 </actions>
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1
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209
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14
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210 <actions>
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211
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212 </actions>
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213
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0
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214 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
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215 <action type="set_environment">
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6
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216 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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15
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217 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
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0
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218 </action>
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219 </actions_group>
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220 </install>
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221 <readme>
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222 AntiSmash installation with all dependencies.
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25
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223 Java needs to be installed.
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0
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224 </readme>
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225 </package>
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226 </tool_dependency>
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