Update docs

[korseby]

Hi there from the PhenoMeNal testing hackathon.

We just modified the demo to run our own test-tool. We encountered the following problems and it would be great if you can change the documentation / tutorial to reflect our problems:

• In the workflow, we needed to add an "input dataset" and connect it with the input of the tool
• The input dataset has to be named and the yaml file has to include that name under inputs
• In the tool options we have to name the output under "Configure Output" and the yaml has to include that name under outputs
• overriding parameters: we need to specify the step number of the tool before the actual parameters, that is not clear in the docs currently

All the best :)

[gregvonkuster]

Trying to install without docker using these instructions http://wft4galaxy.readthedocs.io/installation.html, but docker is still required here: https://github.com/gregvonkuster/wft4galaxy/blob/develop/setup.py#L130, and the docker version requirement results in the requirement for Python 3.5+:

$ python setup.py install
running install
running bdist_egg
running egg_info
creating wft4galaxy.egg-info
writing requirements to wft4galaxy.egg-info/requires.txt
writing wft4galaxy.egg-info/PKG-INFO
writing top-level names to wft4galaxy.egg-info/top_level.txt
writing dependency_links to wft4galaxy.egg-info/dependency_links.txt
writing entry points to wft4galaxy.egg-info/entry_points.txt
writing manifest file 'wft4galaxy.egg-info/SOURCES.txt'
package init file 'templates/__init__.py' not found (or not a regular file)
reading manifest file 'wft4galaxy.egg-info/SOURCES.txt'
writing manifest file 'wft4galaxy.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build

<some logging eliminated here>

Installed /scratch/biotools/galaxy/test/.venv/lib/python2.7/site-packages/sphinx_rtd_theme-0.2.5b1-py2.7.egg
Searching for docker
Reading https://pypi.python.org/simple/docker/
Best match: docker 2.3.0
Downloading https://pypi.python.org/packages/e4/e9/7281d8cc44f3fb2befb13d6d32db30c2bb4b8136e4435459849d70b1ead4/docker-2.3.0.tar.gz#md5=03916d8cb98f567f1f33ab532d87bd72
Processing docker-2.3.0.tar.gz
Writing /tmp/easy_install-ccHjiq/docker-2.3.0/setup.cfg
Running docker-2.3.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-ccHjiq/docker-2.3.0/egg-dist-tmp-r8YhU8
error: Setup script exited with error in docker setup command: Invalid environment marker: python_version < "3.5"

This isn't clear in your base installation instructions. Am I doing something incorrectly?

[kikkomep]

Hi Greg, the requirement for Docker is because the current setup also installs the Docker helper script. In any case, the Python docker library doesn't require Python3.5 (see here).

[gregvonkuster]

Ok, thanks! Not sure why I'm bumping into that issue in my local env.

[ilveroluca]

updates?