Rename shed-install to shed-tools install and add --latest and --revisions flag. Add shed-tools update subcommand.

[rhpvorderman]

Solves #63

Shed-install was diversified into an install and update command. The syntax now is changed.:

• To install: shed-install [flags] -> shed-tools install [flags]
• To update: shed-tools update

This uses built in functionality:

• shed-install shed-tools install already defaulted to the latest installable revision when no revision is given for a tool. The --latest flag forces this behaviour on all tools in the tool list. The latest revision will be installed regardless of the revision in the tool list.
• shed-install --update shed-tools update now uses get_tool_list_from_galaxy to get a tool list from the existing galaxy as a dictionary. Then it does the same as shed-tools install --latest.

To test all three possible methods of tool specifying for shed-install shed-tools install, --revisions was added to allow revisions installation from the command line.

Some other changes had to be made to enable this.

• refactor shed-install shed-tools variables to be more readable
• move some common methods out of shed-install shed-tools to reduce the file length. This includes the logging
• write extra tests
• get_tool_list now does not write a file on instantiation anymore, but instead creates a class that can write a file or just simply give the dictionary.

Other nice changes that resulted from the refactoring:

• run-data-managers and shed-install shed-tools now use the same logging method. Logging can now also be extended to other tools.
• the get_galaxy_connection function was updated so it can optionally also use a file (i.e. a tool_list) to determine connection parameters.
• get_tool_list now uses bioblend api instead of custom connection.
• A check_url method checks the galaxy_url now for get_tool_list and run-data-managers as well broadening the scope of #49

EDIT: 2017-11-27, add changes to reflect further changes. EDIT: 2017-12-27, clarify that --latest works on the whole tool list.

[rhpvorderman]

@jmchilton It would be nice if it could be included in the following ephemeris release. #61 . After someone reviews it of course.

[rhpvorderman]

Done with all the refactoring.

[jmchilton]

Oh wow - this is fantastic!

[mvdbeek]

@rhpvorderman I added some minor tweaks here: https://github.com/rhpvorderman/ephemeris/pull/2

This works really well for me!

[rhpvorderman]

Will now work on making update a subcommand.

[rhpvorderman]

Done with everything except the dummy tool. I do not have time to work on this though. (I only have uploaded one tool in the toolshed and that was some time ago, so this will take quite some time for me to get right again) Can somebody else pick this up? Or we could file an issue and leave this for a later date.

I have altered the message at the top to reflect the further changes.

[bgruening]

This is a great Christmas present for the Galaxy community. Thanks a bunch @rhpvorderman!

xref: https://github.com/galaxyproject/ephemeris/issues/66

[martenson]

Simply great, awesome contribution @rhpvorderman, thank you!