Jupyter docker

[dominikl]

Add a Dockerfile to spin up a Juypiter server with R and customizable version/branch of romero.gateway. This should make it much easier to quickly test snippets, review PRs, etc.

Based on https://github.com/ome/training-notebooks but without installing python, cellprofiler, etc.

/cc @jburel

Test:
What it says in the README.md:
docker build .
docker run -it -p 8888:8888 romero

[jburel]

Test:

• Run docker build -t romero .
• Run docker run -it -p 8888:8888 romero

ERROR:   Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : omero.gateway.exception.DSOutOfServiceException: java.net.ConnectException: Connection refused

ERROR:   Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘connect’ for signature ‘"NULL"’

[dominikl]

Strange, works for me (although I got a weird warning about 'loosing bytes in the JVM'):

> docker build -t romero .
...
Picked up _JAVA_OPTIONS: -Xss2560k -Xmx2g
Rjava.init.warning: lost 5490482 bytes of stack after JVM initialization.

*** Welcome to rOMERO 0.4.5 (~ OMERO 5.4) ***

>
Removing intermediate container 3a39a84bcdc4
 ---> 48ac3281bc4b
Successfully built 48ac3281bc4b
Successfully tagged romero:latest

[jburel]

I will clean everything and try it again. Just in case.

[jburel]

It helps if I build it from the correct location!!

[jburel]

We will probably need an "Hello world" notebook
This can be done in a follow-up PR

[jburel]

Add a note that this library is not needed for r-gateway to work
This is a library used to manipulate pixels data in an example

[jburel]

• Connect the example to outreach
• Use image from R-dataset

Error in normalize(ebimage): could not find function "normalize"

[dominikl]

Ah, I forgot to load the EBImage library, there should be a library(EBImage) after the library(romero.gateway) in the first block. I'll fix it later.

[jburel]

notebook works fine. When comment is added see #68 (review)
this PR will be ready to be merged

[dominikl]

I added the note at the top of the file, because I think EBimage is not the only package which is installed but not strictly necessary for romero.gateway. https://github.com/ome/rOMERO-gateway/pull/68/files#diff-14ee231b27760aa2569d6d117fafef36R1

[jburel]

Thanks