Download and install Cytoscape from a command line ?

[lindfo...@gmail.com]

Hi all,

Is there a way to download and install Cytoscape directly from a command line?
Or is the manual installation from http://www.cytoscape.org/download.php the only option?

I would like to install Cytoscape in a Docker (https://www.docker.com/) image in a way as illustrated in http://docs.docker.com/mac/step_four/.
At least to me it looks a command line Cytoscape installation would be necessary for this.

Thanks,
Erno Lindfors

[Keiichiro Ono]

Hi.

The download page does not work from Dockerfile instructions, but you
can do something like this:

FROM openjdk-8-jdk
RUN mkdir /application
WORKDIR /application
RUN apt-get update && apt-get install -y wget
RUN wget http://chianti.ucsd.edu/cytoscape-3.2.1/cytoscape-3.2.1.tar.gz
RUN tar xfvz http://chianti.ucsd.edu/cytoscape-3.2.1/cytoscape-3.2.1.tar.gz

This creates runnable instance of Cytocape in that directory.

Hope this helps.

Kei

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--
===================================

Keiichiro Ono
http://keiono.github.io/

===================================

[Keiichiro Ono]

Sorry, of course, this line:

RUN tar xfvz http://chianti.ucsd.edu/cytoscape-3.2.1/cytoscape-3.2.1.tar.gz

should be

RUN tar xfvz ./cytoscape-3.2.1.tar.gz

Kei

[lindfo...@gmail.com]

Thanks Kei for your responses, they are very helpful!
Erno

>> email to cytoscape-helpdesk+unsub...@googlegroups.com.

[lindfo...@gmail.com]

Hi Kei and others,

I have been trying to create a simple Cytoscape Docker image by adopting ideas from Kei's code snippet and following a workflow given in http://docs.docker.com/mac/step_four/ but so far have not managed to run it properly.

More specifically, I have included the following code snippet in the Dockerfile:
FROM ubuntu
RUN apt-get update

RUN mkdir /application
WORKDIR /application
RUN apt-get update && apt-get install -y wget
RUN wget http://chianti.ucsd.edu/cytoscape-3.2.1/cytoscape-3.2.1.tar.gz

RUN tar xfvz ./cytoscape-3.2.1.tar.gz
RUN ./cytoscape-unix-3.2.1/cytoscape.sh &

The I have successfully build a Docker image:
sudo docker build -t cyto-test .
Sending build context to Docker daemon  5.12 kB
Step 0 : FROM ubuntu
 ---> 91e54dfb1179
Step 1 : RUN apt-get update
 ---> Using cache
 ---> 998502fcb7f7
Step 2 : RUN mkdir /application
 ---> Using cache
 ---> 830ddaf787a8
Step 3 : WORKDIR /application
 ---> Using cache
 ---> 1fa4a6bfdf5c
Step 4 : RUN apt-get update && apt-get install -y wget
 ---> Using cache
 ---> 60391764108d
Step 5 : RUN wget http://chianti.ucsd.edu/cytoscape-3.2.1/cytoscape-3.2.1.tar.gz
 ---> Using cache
 ---> 4fa221409244
Step 6 : RUN tar xfvz ./cytoscape-3.2.1.tar.gz
 ---> Using cache
 ---> 05c1aefa965a
Step 7 : RUN ./cytoscape-unix-3.2.1/cytoscape.sh &
 ---> Using cache
 ---> 0d77aabdb855
Successfully built 0d77aabdb855

Then I have tried to run the image:
sudo docker run cyto-test

I would expect this should open Cytoscape but nothing happens - Cytoscape does not pop up.

I would guess perhaps this is related to the fact that the Cytoscape opening command ./cytoscape.sh & does work directly from ubuntu command line at least on my computer, I had a long discussion about this for a while back (https://groups.google.com/forum/#!topic/cytoscape-helpdesk/wKNi35tvPds).

As a result of this discussion we came up with a conclusion I can open Cytoscape either by clicking on the icon launcher or by giving a ./Cytoscape & on the command line.

However it seems http://chianti.ucsd.edu/cytoscape-3.2.1/cytoscape-3.2.1.tar.gz does not contain an icon launcher.

Is there any Cytoscape package that contains an icon launcher and that can be downloaded from command line (with wget method)?

Any other ideas how to open Cytoscape from a Docker image?

Thanks,
Erno

[lindfo...@gmail.com]

Hi all,

As an alternative workaround, I recently came across a Dockerfile example from Kei's presentation from VIZBI 2015:
http://www.slideshare.net/keiono/vizbi-2015-tutorial-cytoscape-ipython-docker-and-reproducible-network-data-visualization-workflows
-> Slides 118-119

It seems this example nicely deploys Cytoscape and IPython to a Docker image.

I have been trying to reproduce this example but the execution fails in the following line:
RUN apt-key add graph-tool-pub-key.txt

I am getting the following error message:
gpg: can't open `graph-tool-pub-key.txt': No such file or directory

From what I understand the problem is that the Docker does not recognize the graph-tool-pub-key.txt.

Did you Kei (or anybody else) perhaps do some specific trick (=command) to incorporate the graph-tool-pub-key.txt Docker image?

Thanks,
Erno