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capsules.md
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1 | -# SBGrid software environment |
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1 | +# BioGrids software environment |
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2 | 2 | ## Overview |
3 | 3 | |
4 | -SBGrid is has a new software environment which is significantly faster than the older 'monolithic' shell environment. |
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5 | -This environment includes added features for users to manage their software. |
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6 | -Older features (such as version selection) are still present but improved. |
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7 | -Old scripts should run unaltered and no new commands are required. |
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4 | +BioGrids includes a software environment called the capsule environment. |
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5 | +This software programmatically creates custom environments for every BioGrids application at the time of execution. |
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8 | 6 | |
9 | -## Getting started |
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7 | +Configurations, paths, dependencies and other items needed by the application are created and or set at execution time. The application is then run in this environment. When the application exits the environment is cleaned up and removed. |
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10 | 8 | |
11 | -You can switch from the legacy SBGrid environment to the new with the *sbcap* command. *sbcap on* will enable the capsule environment. |
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12 | -You can always return to the legacy configuration with the *sbcap off* command. |
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13 | - |
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14 | -The sbcap setting is persistent across shells - You don't need to do this for every shell. |
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15 | - |
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16 | -### sbcap - Example |
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17 | -``` |
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18 | -user@linux ~ |
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19 | - $ sbcap on |
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20 | -``` |
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21 | -You will see a notice that you are using the new environment |
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22 | -``` |
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23 | - SBGrid: NEWS |
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24 | -******************************************************************************** |
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25 | - You are using SBGrid capsules. |
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26 | -Capsules provide a simpler, faster, more powerful command line environment with |
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27 | -the same software and commands as the previous SBGrid configuration. |
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28 | -You should not need to change your existing workflow. |
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29 | - |
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30 | -If you experience any issues, please notify us at bugs@sbgrid.org. |
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31 | - For additional information visit https://sbgrid.org/wiki/capsules |
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32 | -******************************************************************************** |
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33 | - Software Support by SBGrid (www.sbgrid.org) |
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34 | -******************************************************************************** |
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35 | -... |
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36 | -``` |
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37 | -## Usage - Capsule Environment for SBGrid |
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38 | -``` |
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39 | -Usage: sbgrid-exectable [ --sbwhich | --sbenv | --sbman | --sbapp:[adlshrH] | --sbcitation | --sbticket | --sbhelp ] |
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40 | - |
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41 | - sbwhich display actual executable path |
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42 | - sbenv display the running environment for the capsule |
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43 | - sbman if it exists, display executable man page |
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44 | - sbapp:[adlshrH] display or select application when executable is in multiple sw titles |
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45 | - :a app run using app |
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46 | - :l list available apps |
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47 | - :s select app from menu |
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48 | - :h short help on apps |
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49 | - :r return codes help related to application selection |
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50 | - :H extended Help |
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51 | - sbcitation TO BE COMPLETED - if applicable, display citation information |
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52 | - sbticket TO BE COMPLETED - collect relevant inforamtion and submit a help request to help@sbgrid.org |
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53 | - sbhelp this message |
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54 | -``` |
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55 | - |
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56 | -### Overrides - managing versions : |
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57 | - |
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58 | -Version overrides may be defined in the ~/.sbgrid.conf file, which will be used each time the sbgrid.[sh|csh] file are sourced. A version override can also be instantiated by simply defining the APP_M prior to capsule execution. |
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59 | - |
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60 | -Setting the version - EXAMPLE |
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61 | - |
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62 | -For the refine executable, the default version show here is 20160324. |
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63 | - |
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64 | -``` |
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65 | - bash-4.1$ refine --sbwhich |
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66 | - /programs/x86_64-linux/buster/20160324/autoBUSTER/bin/linux64/refine |
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67 | -``` |
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68 | - |
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69 | -We can change this by setting the variable BUSTER_X to 20151214 and calling sbwhich in one command : |
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70 | - |
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71 | -``` |
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72 | - bash-4.1$ env BUSTER_X=20151214 refine --sbwhich |
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73 | - /programs/x86_64-linux/buster/20151214/autoBUSTER/bin/linux64/refine |
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74 | -``` |
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75 | -This can also be accomplished by simply setting BUSTER_X=20151214 in the shell or adding the line BUSTER_X=20151214 to your ~/.sbgrid.conf file as [described here](overrides). |
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76 | - |
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77 | -### Managing Duplicate executables |
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78 | -In some cases an executable may exist in multiple applications, i.e. the program *fft* exists in CCP4 **and** Tigris. A default application is already defined based on what executable would be used in the legacy environment, but the user can choose to override this selectively or permanently. |
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79 | - |
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80 | -You can override the default in 4 ways. They are |
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81 | - |
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82 | -1. Command Line arguments selct the application for a single command : |
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83 | - **--sbapp:a <appname>** runs the executable from "appname" or |
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84 | - **--sbapp:s** select application from a list |
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85 | - |
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86 | -2. Environment variable of the form ```_<APPLICATION>```, an underscore followed by executable in UPPER CASE. e.g. ```_XIA2=dials``` will use xia2 executable from "dials". |
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87 | - |
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88 | -3. A User Config_file in *~/.sbgrid_capsule/<execname>*. e.g. echo dials > ~/.sbgrid_capsules/xia2 will uset the shell to always use the xia2 from "dials" |
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89 | - |
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90 | -4. A localsite file in */programs/local/capsule/${SB_ARCH}/defaults/execname* |
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91 | - |
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92 | -### EXAMPLES: |
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93 | -Which executable am I using? |
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94 | - |
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95 | - -bash-4.1 refine --sbwhich |
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96 | - /programs/x86_64-linux/buster/20160324/autoBUSTER/bin/linux64/refine |
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97 | - |
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98 | -What packages include this executable? |
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99 | - |
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100 | - -bash-4.1$ refine --sbapp:l |
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101 | - buster |
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102 | - eman |
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103 | - |
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104 | -refine is present in buster and eman. Where is the eman executable? |
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105 | - |
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106 | - -bash-4.1$ refine --sbapp:a eman --sbwhich |
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107 | - /programs/x86_64-linux/eman/1.9/bin/refine |
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108 | - |
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109 | -or |
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110 | -``` |
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111 | - -bash-4.1$ env _REFINE=eman refine --sbwhich |
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112 | - /programs/x86_64-linux/eman/1.9/bin/refine |
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113 | -``` |
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114 | -I'd like set the eman refine as my default version |
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115 | - |
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116 | - -bash-4.1$ echo eman > ~/.sbgrid_capsule/refine |
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117 | - |
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118 | -Verify that is the case |
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119 | - |
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120 | - -bash-4.1$ refine --sbwhich |
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121 | - /programs/x86_64-linux/eman/1.9/bin/refine |
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122 | - |
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123 | -List all 'refine' executables and select ( and run ) the version from buster |
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124 | - |
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125 | - -bash-4.1$ refine --sbapp:s |
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126 | - 1) buster |
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127 | - 2) eman |
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128 | - 3) Cancel |
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129 | - Please select application 1 |
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130 | - /programs/x86_64-linux/buster/20160324/autoBUSTER/bin/linux64/refine |
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131 | - |
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132 | - |
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133 | -Please report any bugs to bugs@sbgrid.org |
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9 | +The Capsule Environment approach enables a much faster execution environment for users with minimal interference to the users own default shell environment. |