7f8af64bbb4d6c6187fbd3e725a47d43419db253
coot.md
... | ... | @@ -64,23 +64,14 @@ Overrides use this shell variable: CCP4_X |
64 | 64 | We are running `coot` from ccp4 version 7.1 and there are several other versions available. |
65 | 65 | |
66 | 66 | ### Changing the application that provides coot - overriding default titles |
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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67 | +SBGrid uses CCP4's `coot` by default, but that can be changed with a configuration file in the ~/.sbgrid_capsules directory. A default title can be specified for any duplicate executable by creating a file with the **name of the executable** that contains a single line with the name of the application. For coot this would be: |
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69 | 68 | |
70 | - export _COOT=coot |
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69 | + mkdir -p ~/.sbgrid_capsule |
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70 | + echo echo > ~/.sbgrid_capsule/coot |
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71 | 71 | |
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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72 | +If we do this, we can see: |
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81 | 73 | |
82 | 74 | ``` |
83 | -$ export _COOT=coot |
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84 | 75 | $ coot --sbwhich |
85 | 76 | /programs/x86_64-linux/coot/0.9.1/bin/coot |
86 | 77 | ``` |
... | ... | @@ -90,7 +81,7 @@ Now `coot` comes from the applciation title **coot**. The default version there |
90 | 81 | Let's switch to CCPEM as the provider of the `coot` program. |
91 | 82 | To do that we just set the variable: |
92 | 83 | ``` |
93 | -$ export _COOT=ccpem |
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84 | +$ echo ccpem > ~/.sbgrid_capsule/coot |
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94 | 85 | |
95 | 86 | $ coot --sbwhich |
96 | 87 | /programs/x86_64-linux/ccpem/1.4.1/bin/coot |
... | ... | @@ -131,7 +122,7 @@ To use coot from CCPEM version 1.3.0, we set the CCPEM_X variable to 1.3.0 |
131 | 122 | Set the title for the `coot` executable to "coot" to use Paul Emsley's builds for linux : |
132 | 123 | |
133 | 124 | ``` |
134 | - $ export _COOT=coot |
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125 | +echo echo > ~/.sbgrid_capsule/coot |
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135 | 126 | |
136 | 127 | $ coot --version |
137 | 128 | 0.9.1 (revision-count 10157) |
... | ... | @@ -154,7 +145,7 @@ This is the latest version. To switch to an older version, just set the COOT_X v |
154 | 145 | Now, let's change `coot` to come from CCP4 and check the version : |
155 | 146 | |
156 | 147 | ``` |
157 | - $ export _COOT=ccp4 |
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148 | +echo echo > ~/.sbgrid_capsule/ccp4 |
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158 | 149 | |
159 | 150 | $ coot --version |
160 | 151 | 0.9 (revision-count 9932) |
... | ... | @@ -168,4 +159,4 @@ The version of `coot` changes to the version provided by the CCP4 version specif |
168 | 159 | |
169 | 160 | For more info, see [capsules](capsules), and [version manangement](overrides). |
170 | 161 | |
171 | -For questions or to report bugs, please email bugs@sbgrid.org |
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0 | +For questions or to report bugs, please email bugs@sbgrid.org |