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coot.md
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1 | +# Setting COOT title and version in SBGrid |
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2 | +COOT is present in several titles and many versions in SBGrid. Selecting the application and version of the `coot` executable can be accomplished on-the-fly in a single step in the SBGrid capsule environment. Here are some examples of managing COOT in SBGrid capsules, but this should work for any application with duplicate executables and multiple versions. |
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3 | + |
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4 | +To confirm that capsules are enabled, run |
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5 | + |
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6 | +``` |
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7 | +sbcap status |
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8 | +``` |
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9 | + |
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10 | +If capsules are enabled, the output should be : |
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11 | + |
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12 | +``` |
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13 | + $ sbcap status |
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14 | +Active |
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15 | +``` |
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16 | + |
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17 | +If capsules are InActive, they can be enable with the `sbcap on` command followed by `source /programs/sbgrid.shrc`. |
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18 | + |
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19 | + |
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20 | +### "Which COOT am I using?" |
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21 | +The `sbwhich` command will show which `coot` executable is in use : |
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22 | + |
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23 | +``` |
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24 | +$ sbwhich coot |
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25 | +/programs/x86_64-linux/ccp4/7.1/ccp4-7.1/bin/coot |
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26 | +``` |
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27 | + |
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28 | +or alternatively the `--sbwhich` flag can be used |
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29 | + |
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30 | +``` |
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31 | +$ coot --sbwhich |
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32 | +/programs/x86_64-linux/ccp4/7.1/ccp4-7.1/bin/coot |
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33 | +``` |
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34 | + |
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35 | +By default we use the CCP4 release of COOT in SBGrid. This version is stable, supported and the same for MacOS and Linux. But it is easy to change. |
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36 | + |
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37 | +### Next, what titles provide "coot" executables? |
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38 | +SBGrid capsules provide an additional set of flags for all executables, prefixed with `--sbapp:`. For more info see the [documentation for capsules here.](capsules.md) To list all the installed tiles that provide `coot`, use `--sbapp:l` |
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39 | + |
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40 | +``` |
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41 | +$ coot --sbapp:l |
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42 | + ccp4 |
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43 | + ccpem |
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44 | + coot |
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45 | +``` |
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46 | + |
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47 | +The executable `coot` is present in the titles **ccp4, ccpem, and coot**. |
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48 | + |
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49 | +### What version does this coot executable come from? |
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50 | +Running *sbgrid-info -l* will print the available versions for a title. |
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51 | + |
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52 | +``` |
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53 | + $ sbgrid-info -l ccp4 |
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54 | + Version information for: /programs/x86_64-linux/ccp4 |
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55 | + |
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56 | +Default version: 7.1 |
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57 | +In-use version: 7.1 |
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58 | + |
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59 | +Installed versions: 7.1 7.1.006 7.0 7.0.078 6.3.0 |
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60 | +Other available versions: 7.1.006 7.0 7.0.078 6.3.0 |
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61 | +Overrides use this shell variable: CCP4_X |
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62 | +``` |
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63 | + |
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64 | +We are running `coot` from ccp4 version 7.1 and there are several other versions available. |
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65 | + |
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66 | +### Changing the application that provides coot - overriding default titles |
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67 | +SBGrid uses CCP4's `coot` by default, but that can be changed with an environmental variable. A default title can be specified for any duplicate executable with the `<_EXECUTABLE>` variable where `<EXECUTABLE>` is the **all-capital** name of the executable. |
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68 | +For example, since `coot` comes from CCP4 by default, we can change it to CCPEM by setting : |
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69 | + |
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70 | + export _COOT=coot |
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71 | + |
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72 | +for bash, or |
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73 | + |
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74 | + setenv _COOT coot |
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75 | + |
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76 | +for tcsh users. |
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77 | + |
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78 | +`_COOT` is the executable name, `coot` is the name of the title that will provide the program when we run `coot`. |
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79 | + |
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80 | +If we do this, we can see (in bash) |
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81 | + |
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82 | +``` |
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83 | +$ export _COOT=coot |
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84 | +$ coot --sbwhich |
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85 | +/programs/x86_64-linux/coot/0.9.1/bin/coot |
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86 | +``` |
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87 | + |
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88 | +Now `coot` comes from the applciation title **coot**. The default version there is 0.9.1. |
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89 | + |
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90 | +Let's switch to CCPEM as the provider of the `coot` program. |
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91 | +To do that we just set the variable: |
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92 | +``` |
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93 | +$ export _COOT=ccpem |
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94 | + |
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95 | +$ coot --sbwhich |
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96 | +/programs/x86_64-linux/ccpem/1.4.1/bin/coot |
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97 | + |
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98 | + $ coot --version |
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99 | +0.9-pre (revision-count 0) |
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100 | +[with guile 1.8.8 embedded] |
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101 | +[with python 2.7.15 embedded] |
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102 | +Builder_info: CCP-EM, Oxfordshire, UK |
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103 | +Binary type: Linux-x86_64-scientific-linux-6.10-python-gtk2 |
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104 | +``` |
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105 | + |
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106 | +### Setting the version |
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107 | +The version of a title is set by the `<TITLE_X>` variable where `<TITLE>` is the title of an application in uppercase. You can see this variable in the `sbgrid-info -l` output. |
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108 | + |
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109 | +``` |
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110 | + $ sbgrid-info -l ccpem |
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111 | + Version information for: /programs/x86_64-linux/ccpem |
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112 | + |
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113 | +Default version: 1.4.1 |
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114 | +In-use version: 1.4.1 |
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115 | + |
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116 | +Installed versions: 1.4.1 1.4.0 1.3.0 20200722 |
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117 | +Other available versions: 1.4.0 1.3.0 20200722 |
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118 | +Overrides use this shell variable: CCPEM_X |
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119 | +``` |
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120 | + |
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121 | +To use coot from CCPEM version 1.3.0, we set the CCPEM_X variable to 1.3.0 |
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122 | + |
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123 | +``` |
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124 | + $ export CCPEM_X=1.3.0 |
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125 | + |
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126 | + $ sbwhich coot |
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127 | +/programs/x86_64-linux/ccpem/1.3.0/bin/coot |
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128 | +``` |
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129 | + |
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130 | +`coot` has a --version flag that can be used to confirm the version |
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131 | +Set the title for the `coot` executable to "coot" to use Paul Emsley's builds for linux : |
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132 | + |
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133 | +``` |
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134 | + $ export _COOT=coot |
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135 | + |
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136 | + $ coot --version |
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137 | +0.9.1 (revision-count 10157) |
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138 | +[with guile 1.8.8 embedded] |
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139 | +[with python 2.7.15 embedded] |
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140 | +Builder_info: built by: Paul Emsley build-host: charybdis on: Wed 21 Oct 0247.16 BST 2020 |
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141 | +Binary type: Linux-x86_64-scientific-linux-7.6-python-gtk2 |
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142 | +``` |
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143 | + |
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144 | +This is the latest version. To switch to an older version, just set the COOT_X variable to that version: |
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145 | + |
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146 | +``` |
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147 | + $ export COOT_X=0.8.8 |
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148 | + |
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149 | + $ coot --version |
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150 | +0.8.8 (revision-count 6690) |
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151 | +[with guile 1.8.8 embedded] |
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152 | +``` |
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153 | + |
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154 | +Now, let's change `coot` to come from CCP4 and check the version : |
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155 | + |
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156 | +``` |
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157 | + $ export _COOT=ccp4 |
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158 | + |
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159 | + $ coot --version |
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160 | +0.9 (revision-count 9932) |
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161 | +[with guile 1.8.8 embedded] |
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162 | +[with python 2.7.16 embedded] |
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163 | +Builder_info: CCP4, Oxfordshire |
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164 | +Binary type: Linux-x86_64-scientific-linux-6.10-python-gtk2 |
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165 | +``` |
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166 | + |
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167 | +The version of `coot` changes to the version provided by the CCP4 version specified by CCP4_X. |
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168 | + |
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169 | +For more info, see [capsules](capsules.md), and [version manangement](overrides.md). |
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170 | + |
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171 | +For questions or to report bugs, please email bugs@sbgrid.org |
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