- fixed TOC in capsules.md and updated to match opening message. Changed section headers to H2 for modulfiles.md

- [Managing Duplicate executables](#usage-capsule-environment-for-sbgrid_managing-duplicate-executables)

- [EXAMPLES:](#usage-capsule-environment-for-sbgrid_examples)

## Overview

SBGrid is has a new software environment which is significantly faster than the older 'monolithic' shell environment.

**Check out Carol Herre's [presentation on Capsules on SBGrid TV](https://www.youtube.com/watch?v=baexe9R128A)**

## Getting started

You can switch from the legacy SBGrid environment to the new with the *sbcap* command. *sbcap on* will enable the capsule environment.

The sbcap setting is persistent across shells - You don't need to do this for every shell.

### sbcap - Example

```

user@linux ~

$ sbcap on

```

You will see a notice that you are using the new environment

********************************************************************************

Software Support by SBGrid (www.sbgrid.org)

********************************************************************************

...

```

## Usage - Capsule Environment for SBGrid

```

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

sbhelp this message

```

### Overrides - managing versions :

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.

```

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).

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.

You can override the default in 4 ways. They are

4. A localsite file in */programs/local/capsule/${SB_ARCH}/defaults/execname*

### EXAMPLES:

Which executable am I using?

- [Issues](#issues)

<a name="overview"></a>

Modulefiles for loading and unloading the sbgrid or biogrids environment are available in /programs/share/modulefiles/x86_64-linux and /programs/share/modulefiles/i386-mac. The module files are designed to work with an existing module/lmod setup. Loading the sbgrid/biogrids module initializes the entire sbgrid/biogrids environment and is used instead of the "source" command. If you are using modules then you should remove the source lines, such as "source sbgrid.shrc", from your startup rc files.

<a name="access"></a>

To access the files you need to update your **MODULEPATH** environment variable.

The above command may be added to your shell startup files or your site Administrator may update the system wide path.

<a name="verify"></a>

***module avail*** will show you what modules are available for loading. If your MODULEPATH is correct you should see the sbgrid/rc and/or the biogrids/rc module.

<a name="load"></a>

Loading the sbgrid/biogrids module initializes the entire environment and not individual applications. The module determines if you are using bash or tcsh and loads the shell appropriate environment using the same command for both tcsh and bash.

<a name="unload"></a>

You can remove the sbgrid/biogrids environment with the ***module unload*** command. This removes any grid specific environment settings. If after loading sbgrid you load additonal modules, these modules will not be removed. To see what modules you have loaded you can use ***module list***.

UnLoading SBGrid

<a name="issues"></a>

Please report any issues to bugs@sbgrid.org