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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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9
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4 <repository changeset_revision="5a449da71d08" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://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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9
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7 <repository changeset_revision="a44693e3a2c4" name="package_hmmer_3_0" owner="iuc" toolshed="http://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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6
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10 <repository changeset_revision="ce304c51f69b" name="package_muscle_3_8_31" owner="bgruening" toolshed="http://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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13 <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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14 </package>
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15
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17
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16
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17 <package name="helperlibs" version="0.1.2">
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7
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18 <install version="1.0">
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5
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19 <actions>
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17
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20 <action type="download_by_url">https://pypi.python.org/packages/source/h/helperlibs/helperlibs-0.1.2.tar.gz</action>
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21 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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22 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
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23 <action type="set_environment">
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24 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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25 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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26 </action>
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5
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27 </actions>
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28 </install>
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29 <readme>
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17
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30 helperlibs python library
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31 </readme>
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32 </package>
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18
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33
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21
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34 <package name="cssselect" version="0.9">
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35 <install version="1.0">
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36 <actions>
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37 <action type="download_by_url">https://pypi.python.org/packages/source/c/cssselect/cssselect-0.9.tar.gz</action>
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38 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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39 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
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40 <action type="set_environment">
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41 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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42 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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43 </action>
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44 </actions>
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45 </install>
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46 <readme>
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47 cssselect python library
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48 </readme>
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49 </package>
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50
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18
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51 <package name="pyquery" version="1.2.6">
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52 <install version="1.0">
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53 <actions>
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20
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54 <action type="download_by_url">https://github.com/gawel/pyquery/archive/1.2.6.tar.gz</action>
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18
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55 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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56 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
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57 <action type="set_environment">
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58 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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59 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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60 </action>
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61 </actions>
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62 </install>
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63 <readme>
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21
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64 pyquery python library
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18
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65 </readme>
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66 </package>
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67
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17
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68 <package name="straight.plugin" version="1.4.0-post-1">
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69 <install version="1.0">
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70 <actions>
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71 <action type="download_by_url">https://pypi.python.org/packages/source/s/straight.plugin/straight.plugin-1.4.0-post-1.tar.gz</action>
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72 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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73 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
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74 <action type="set_environment">
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75 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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76 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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77 </action>
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78 </actions>
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79 </install>
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80 <readme>
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81 straight.plugin python library
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5
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82 </readme>
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0
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83 </package>
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84 <package name="antismash" version="2.0.2">
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85 <install version="1.0">
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86 <actions_group>
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87 <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. -->
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8
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88 <actions architecture="x86_64" os="darwin">
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89 <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action>
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90 <action type="move_directory_files">
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91 <source_directory>.</source_directory>
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92 <destination_directory>$INSTALL_DIR</destination_directory>
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93 </action>
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94 <action type="chmod">
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95 <file mode="750">$INSTALL_DIR/run_antismash.py</file>
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96 </action>
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16
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97 <!-- AntiSmash has a prerequirement check that is not useful for us, because we
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98 do not offer the option for genprediction and do not install glimmer and Co.
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99 For that reason deactivate the check.
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100 -->
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17
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101 <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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102 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
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103 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
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8
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104 </actions>
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105 <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. -->
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106 <actions architecture="i386" os="darwin">
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0
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107 <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action>
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108 <action type="move_directory_files">
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109 <source_directory>.</source_directory>
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110 <destination_directory>$INSTALL_DIR</destination_directory>
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111 </action>
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112 <action type="chmod">
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113 <file mode="750">$INSTALL_DIR/run_antismash.py</file>
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114 </action>
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16
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115 <!-- AntiSmash has a prerequirement check that is not useful for us, because we
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116 do not offer the option for genprediction and do not install glimmer and Co.
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117 For that reason deactivate the check.
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118 -->
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17
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119 <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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120 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
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121 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
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0
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122 </actions>
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123 <!-- Download the binaries for AntiSmash compatible with 64-bit Linux. -->
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6
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124 <actions architecture="x86_64" os="linux">
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7
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125 <action target_filename="antismash-2.0.2.tar.bz2" type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.x86_64.tar.bz2</action>
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12
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126 <action type="move_directory_files">
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127 <source_directory>.</source_directory>
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128 <destination_directory>$INSTALL_DIR</destination_directory>
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129 </action>
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0
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130 <action type="chmod">
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131 <file mode="750">$INSTALL_DIR/run_antismash.py</file>
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132 </action>
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15
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133 <!-- AntiSmash has a prerequirement check that is not useful for us, because we
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134 do not offer the option for genprediction and do not install glimmer and Co.
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135 For that reason deactivate the check.
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136 -->
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17
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137 <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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138 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
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139 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
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22
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140 <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and
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141 we need to copy this plugin into the correct location.
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142 -->
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143 <action type="move_directory_files">
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144 <source_directory>$REPOSITORY_INSTALL_DIR/src/</source_directory>
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145 <destination_directory>$INSTALL_DIR/antismash/output_modules/</destination_directory>
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146 </action>
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0
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147 </actions>
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148 <!-- Download the binaries for AntiSmash compatible with 32-bit Linux. -->
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6
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149 <actions architecture="i386" os="linux">
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0
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150 <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.i686.tar.bz2</action>
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151 <action type="move_directory_files">
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152 <source_directory>.</source_directory>
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153 <destination_directory>$INSTALL_DIR</destination_directory>
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154 </action>
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155 <action type="chmod">
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156 <file mode="750">$INSTALL_DIR/run_antismash.py</file>
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157 </action>
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16
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158 <!-- AntiSmash has a prerequirement check that is not useful for us, because we
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159 do not offer the option for genprediction and do not install glimmer and Co.
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160 For that reason deactivate the check.
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161 -->
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17
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162 <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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163 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
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164 <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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165 </actions>
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1
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166
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14
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167 <actions>
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168
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169 </actions>
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170
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0
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171 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
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172 <action type="set_environment">
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6
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173 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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15
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174 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
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0
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175 </action>
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176 </actions_group>
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177 </install>
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178 <readme>
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179 AntiSmash installation with all dependencies.
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180 </readme>
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181 </package>
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182 </tool_dependency>
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