Machine Polish - Review Before GCC2018

[jmchilton]

Must Fix Bugs

• Tool shed installs broken - Cannot install from Tool Shed in Virtual Appliance planemo#742.

TODO

• Update samtools on the machine - the Planemo docs are complicated a bit because they expect a very old version of samtools - xref Update bwa test data generation to allow old or new samtools to be used. planemo#697.

Older Items to Consider:

• Install bioblend-tutorial and place link on Desktop - https://github.com/nsoranzo/bioblend-tutorial (https://github.com/galaxyproject/planemo-machine/blob/master/roles/galaxyprojectdotorg.devbox/tasks/main.yml)
• ensure docker images for IEs are pulled (maybe... -John)
• add env var $GALAXY_ROOT or update documentation to use $GALAXY
• Install galaxy-parsec.
• Update ansible in the machine.
• ensure that the tool_conf.xml is writable.
  • fewer levels of indirection here? There is a non-sample tool_conf.xml, but the real tool_conf is "dev_tool_conf.xml" which loads tools from a folder, it is very complex...