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The Galaxy Tool Shed (referred to colloquially in Planemo as the “shed”) can store Galaxy tools, dependency definitions, and workflows among other Galaxy artifacts. This guide will assume some basic familiarity with the shed - please review the Tool Shed Wiki for an introduction.

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Before getting started, it is a good idea to have accounts on the Galaxy and (optionally) Tool Sheds. Also, if you haven’t initialized a global Planemo configuration file ( ~/.planemo.yml ) this can be done with.

This will populate a template ~/.planemo.yml file and provide locations to fill in shed credentials for the test and main Tool Sheds. For each shed, fill in either an API key or an email and password . Also specify the shed_username created when registering shed accounts. All these options can be specified and/or overridden on each planemo command invocation - but that becomes tedious quickly.

Planemo can be used to used to publish “repositories” to the Tool Shed. A single GitHub repository or locally managed directory of tools may correspond to any number of Tool Shed repositories. Planemo maps files to Tool Shed repositories using a special file called .shed.yml .

From a directory containing tools, a package definition . etc… the shed_init command can be used to bootstrap a new .shed.yml file.

There is not a lot of magic happening here, this file could easily be created directly with a text editor - but the command has a --help to assist you and does some very basic validation.


Periods and hyphens are disallowed in repository names, it is recommended replacing periods in the version number with underscores.

The following naming conventions are recommended and in some cases Planemo will determine the repository type based on adherence to these conventions (for packages and suites specifically).

More information on .shed.yml can be found as part of the IUC best practice documentation .

After reviewing .shed.yml , this configuration file and relevant shed artifacts can be quickly linted using the following command.

Once the details the .shed.yml are set and it is time to create the remote repository and upload artifacts to it - the following two commands can be used - the first only needs to be run once and creates the repository based the metadata in .shed.yml and the second uploads your actual artifacts to it.

In practice, biharmonic viscosity and diffusivity allow a less viscous, yet numerically stable, simulation than harmonic viscosity and diffusivity. However, there is no physical rationale for such operators being of leading order, and more boundary conditions must be specified than for the harmonic operators. If one considers the approximations of (2.157) - (2.160) and (2.170) - (2.173) to be terms in the Taylor series expansions of the eddy terms as functions of the large-scale gradient, then one can argue that both harmonic and biharmonic terms would occur in the series, and the only question is the choice of coefficients. Using biharmonic viscosity alone implies that one zeros the first non-vanishing term in the Taylor series, which is unsupported by any fluid theory or observation.

Nonetheless, MITgcm supports a plethora of biharmonic viscosities and diffusivities, which are controlled with parameters named similarly to the harmonic viscosities and diffusivities with the substitution h 4 in the MITgcm parameter name. MITgcm also supports biharmonic Leith and Smagorinsky viscosities:

(2.174) A 4 S m a g = ( v i s c C 4 S m a g π ) 2 L 4 8 | D |
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A 4 L e i t h = L 5 8 ( v i s c C 4 L e i t h π ) 6 | ¯ ω 3 | 2 + ( v i s c C 4 L e i t h D π ) 6 | ¯ ˜ u h | 2

However, it should be noted that unlike the harmonic forms, the biharmonic scaling does not easily relate to whether energy-dissipation or enstrophy-dissipation scales are resolved. If similar arguments are used to estimate these scales and scale them to the gridscale, the resulting biharmonic viscosities should be:

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State: California

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State: Colorado

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State: Wisconsin

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State: Georgia

Title: Georgia Campus Free Speech Act


State: Illinois

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State: Michigan

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