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minor touch of readme

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martenson committed Jun 27, 2016
1 parent 606cc5c commit 725b232c629e610a699a2e782d57ee18f14be460
Showing with 32 additions and 27 deletions.
  1. +20 −20 README.rst
  2. +12 −7 docs/appliance.rst
@@ -33,27 +33,27 @@ develop Galaxy tools.
Obtaining Planemo
-----------------

Planemo can be installed via Conda, Homebrew, or
as a more traditional Python project.

To install using Conda_:
The recommended approach for installing Planemo is to use Homebrew_ or
linuxbrew_. To install Planemo this way use the ``brew`` command as
follows.

::

$ conda config --add channels r
$ conda config --add channels bioconda
$ conda install planemo
$ brew tap galaxyproject/tap
$ brew install planemo

To install using Homebrew_ or linuxbrew_:

Planemo can alternatively be installed via Conda_:

::

$ brew tap galaxyproject/tap
$ brew install planemo
$ conda config --add channels r
$ conda config --add channels bioconda
$ conda install planemo

For a more traditional Python installation set up a virtualenv
for ``planemo`` (this example creates a new one in ``.venv/``) and then
install with ``pip``.
For third option and a more traditional Python installation set up a virtualenv
for Planemo (this example creates a new one in ``.venv/``) and then
install it with ``pip``.

::

@@ -69,8 +69,8 @@ You can choose from open virtualization format (OVA_, .ova), Docker, or Vagrant
Planemo Basics
--------------

This quick start will assume you will have a directory with one or more
tool XML files. If none is available, one can be quickly create for
This quick start will assume you have a directory with one or more
tool XML files. If none is available, one can be quickly created for
demonstrating ``planemo`` as follows ``mkdir mytools; cd mytools; planemo
project_init --template=demo``.

@@ -81,7 +81,6 @@ practices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/
::

$ planemo lint
...

Like many ``planemo`` commands - by default this will search the
current directory and use all tool files it finds. It can be explicitly
@@ -92,14 +91,14 @@ passed a path to tool files or a directory of tool files.
$ planemo l randomlines.xml

The ``lint`` command takes in additional options related to
reporting levels, exit code, etc. These options are described here
or (like all available commands) can be accessed by passing ``--help`` to it.
reporting levels, exit code, etc. These options are described
in the `docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
or (like with all commands) can be accessed by passing ``--help`` to it.

::

$ planemo l --help
Usage: planemo lint [OPTIONS] TOOL_PATH
...

Once tools are syntactically correct - it is time to test. The ``test``
`command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__
@@ -121,7 +120,8 @@ testing. Pass ``--install_galaxy`` instead of ``--galaxy_root``.
$ planemo t --install_galaxy

Planemo will create a HTML output report in the current directory named
``tool_test_output.html`` (override with ``--test_output``). See an `example <http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index>`_
``tool_test_output.html`` (override with ``--test_output``). See an
`example <http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index>`_
of such a report for Tophat.

Once tools have been linted and tested - the tools can be viewed in a
@@ -3,8 +3,8 @@ Virtual Appliance
==================

You can use Planemo as part of a Galaxy tool development virtual
appliance pre-configured with Planemo, Galaxy_, Docker_, a local Tool Shed,
linuxbrew_, and Komodo_ editor.
appliance which comes pre-configured with Planemo, Galaxy_, Docker_, Conda_,
a local Tool Shed, linuxbrew_, Komodo_ and Atom_ editors.


Quick Links
@@ -34,7 +34,7 @@ format (OVA_, .ova), Docker, Vagrant, and as a Google Compute Engine cloud image

The OVA image is a stable way to boot a Planemo virtual
machine on any platform and comes with a pre-configured Xubuntu-based windowed
operating system with graphical editing tools including Komodo_ editor.
operating system with graphical editing tools including Komodo_ and Atom_ editors.
This approach can be thought of more as a complete
environment and may be better for tutorials and workshops where consistent user
experience is more important.
@@ -49,12 +49,12 @@ local compute resources are unavailable or insufficient.

Launching the Appliance
-----------------------
The following sections will desribe how to launch the appliance using various platforms.
The following sections will describe how to launch the appliance using various platforms.

Launching the Appliance (VirtualBox - OVA)
================================================

The VirtualBox OVA variant of the planemo appliance comes preconfigured with
The VirtualBox OVA variant of the Planemo appliance comes preconfigured with
a full windowed development environment (based on Xubuntu). Encompassing the
complete environment means it is easier to setup and provides an identical
experience for every developer using it. These make the OVA image ideal
@@ -78,7 +78,7 @@ and the machine should become available.
.. image:: images/ova_importing.png
:alt: Screenshot OVA Import

The Firefox browser, Komodo_ editor, Galaxy, Planemo and everything else is
The Firefox browser, Komodo_ and Atom_ editors, Galaxy, Planemo and everything else is
available right away on the desktop along with useful links.

.. image:: images/ova_desktop.png
@@ -159,6 +159,7 @@ following command (which will pull the appliance down from `Docker Hub
<https://registry.hub.docker.com/u/planemo/interactive/>`_).

::

$ docker run -p 8010:80 -p 9009:9009 -v `pwd`:/opt/galaxy/tools -i -t planemo/interactive

This command will start Galaxy and various other services and then open a bash
@@ -193,6 +194,7 @@ This file must literally be named ``Vagrantfile``. Next you will need to
startup the appliance. This is as easy as

::

$ vagrant up

Once the virtual server has booted up completely, Galaxy will be available at
@@ -218,6 +220,7 @@ If you set these defaults, you will not have to supply them to all subsequent
commands.

::

$ gcloud auth login
$ gcloud config set project YOUR-PROJECT-NAME
$ gcloud config set compute/region us-central1 (replace us-central1 with another region if desired)
@@ -228,13 +231,14 @@ need to be done one time, unless you delete the image from your account.

::

gcloud compute images create planemo-machine --source-uri=http://storage.googleapis.com/galaxyproject_images/planemo_machine.image.tar.gz
$ gcloud compute images create planemo-machine --source-uri=http://storage.googleapis.com/galaxyproject_images/planemo_machine.image.tar.gz

To launch the image as a fresh instance, use the following command. This
command will, upon completion, display an external ip address that you can
navigate to in your web browser.

::

$ gcloud compute instances create planemo --machine-type n1-standard-2 --image planemo-machine --tags http-server

If you'd like to SSH in to the instance at this point, it's easy to do with:
@@ -264,4 +268,5 @@ environments such as Amazon Web Services and Google Compute Engine.
.. _Kitematic: https://kitematic.com/
.. _boot2docker: http://boot2docker.io/
.. _OVA: https://en.wikipedia.org/wiki/Open_Virtualization_Format
.. _Atom: https://atom.io/

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