Some notes going into the Documentation meeting at Brandeis, 1/31/2017-2/2/2017.

Location of documentation

Documentation will live in, which will be redesigned. The domain points to The page is technically not a wiki but close enough.


Start with a blank slate and figure out the exact procedures for creating a LAPPS Grid.

In particular, what needs to be done for the following to happen:

Installing a service manager

Requirements (debian, rhel, osx), start with virgin machine (JetStream instance)

Here are some [historical notes] from ( from 2014.

There is a one-step-install script (written by Keith for debian/ubuntu, Keigh had a RHEL version).

Now an easier proces:

**set up new service manager on Jetstream

Creating and adding services

How to create services - wrapping, discriminators, LIF, WSEV, deploying, registering



Vocabulary and Discriminators:

check whether this all still works

Discriminators are used in the produces and requires sections of a tool wrapper’s metadata. It is up to the tool wrapper to check whether input has what it needs (searching the contains section of the metadata section of a view. THere is also a discriminator handed in with the Data structure, which has a discriminator and a payload section. The dicriminator there is one of the dozen or so media discriminators in (for example, the discriminator gate which refers to


THis is explained in the wrapping manual in, which was listed above.

After deploying a war file to tomcat the new war will be deployed automatically, but if you changed Java versions while running a tomcat server then you do need to restart Tomcat.


Setting up Galaxy


No documentation available. We first need to get everything on the latest service manager.

Making services run on https

Some MV notes somewhere

Authorization of data services (LDC)

This is actually just a token header that is put in …

How to create Docker images

Running on AWS

Running on JetStream

There is a bash script at

Keigh + Marc: review ow to do that from Keith’s example a few months ago

Creating a lappsgrid with appliances

Using Ansible

Conda, toolshed and friends

Using Jupyter



Where are all the repositories, what do they do and what is their role in the bigger picture

Goals for first day

Do not get lost in details, expand on the list above and get an overview of each item, filling in all we know and collecting in the wiki, by copying in text or by providing links, all information that is relevant and noting what information is missing.

Layout of basic redesign of

Come up with scenarios of what somebody may want to do given some configuration. For example: