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capsules.md
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1 | +# SBGrid software environment |
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2 | +## Overview |
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3 | + |
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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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8 | + |
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9 | +## Getting started |
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10 | + |
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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 |