capsules

SBGrid software environment

SBGrid is has a new environment which is significantly faster than the old shell environment. It also includes added features for users to manage their software. Older features (such as version selection) are still present as well.

Overview

Usage - Capsule Environment for SBGrid

Usage: sbgrid-exectable  [ --sbwhich | --sbenv | --sbman | --sbapp:[adlshrH] | --sbcitation | --sbticket | --sbhelp ]

 sbwhich         display actual executable path
 sbenv           display the running environment for the capsule
 sbman           if it exists, display executable man page
 sbapp:[adlshrH] display or select application when executable is in multiple sw titles
      :a app     run using app
      :l         list available apps
      :s         select app from menu
      :h         short help on apps
      :r         return codes help related to application selection
      :H         extended Help 
 sbcitation      TO BE COMPLETED - if applicable, display citation information
 sbticket        TO BE COMPLETED - collect relevant inforamtion and submit a help request to help@sbgrid.org
 sbhelp          this message

Overrides:

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 defining the APP_M prior to capsule execution.

    EXAMPLE: (all examples in bash)

        bash-4.1$ refine --sbwhich
        /programs/x86_64-linux/buster/20160324/autoBUSTER/bin/linux64/refine

        bash-4.1$  env BUSTER_X=20151214 refine --sbwhich
        /programs/x86_64-linux/buster/20151214/autoBUSTER/bin/linux64/refine

Duplication of executables

In some cases an executable may exist in multiple applications. A default application is already defined based upon what executable would be used in the legacy environment, but the user can choose to override this selectively or permanently.

You can override the default in 4 ways. They are

1. Command Line arguments: "--sbapp:a appname" runs the executable from "appname" or "--sbapp:s" select application from a list
2. Environment VAR - an '_'(underscore) followed by executable in UPPER CASE. e.g. "_XIA2=dials" will use xia2 executable from "dials"
   
3. User Config_file in ~/.sbgrid_capsule/execname. e.g. echo dials > ~/.sbgrid_capsules/xia2 will use the xia2 from "dials"
4. A localsite file in /programs/local/capsule/${SB_ARCH}/defaults/execname

EXAMPLES: Which executable am I using?

 -bash-4.1 refine --sbwhich
 /programs/x86_64-linux/buster/20160324/autoBUSTER/bin/linux64/refine

What packages include this executable?

-bash-4.1$ refine --sbapp:l
    buster
    eman

refine is present in buster and eman. Where is the eman executable?

-bash-4.1$ refine --sbapp:a eman --sbwhich
/programs/x86_64-linux/eman/1.9/bin/refine

or

-bash-4.1$ env _REFINE=eman refine --sbwhich
/programs/x86_64-linux/eman/1.9/bin/refine

I'd like set the eman refine as my default version

-bash-4.1$ echo eman > ~/.sbgrid_capsule/refine

Verify that is the case

-bash-4.1$ refine --sbwhich
/programs/x86_64-linux/eman/1.9/bin/refine

List all 'refine' executables and select ( and run ) the version from buster

-bash-4.1$ refine --sbapp:s --sbwhich
1) buster
2) eman
3) Cancel
Please select application 1
/programs/x86_64-linux/buster/20160324/autoBUSTER/bin/linux64/refine