koadman/docker-A5-miseq — pull request #1 by michaelbarton (2014-09-16 05:57:38+00:00)
Title: Working version of image

Thanks for making this Aaron. I'm very excited that you would take the time to create an assembler image of A5. We have been testing A5 at the JGI so it would be very useful to include this in the nucleotid.es benchmarks.

This pull request contains a few critical changes and some minor cosmetic ones. The critical ones are

* Install the java run time as some tools as part of A5 require it.
* Run the a5 pipeline in a temporary directory. There was some issue with directories not being created because I think the prefix you pass to A5 should not be an existing directory. Perhaps I am wrong here though.

The rest are minor changes

* Remove non-required dependencies such as gcc etc.
* Remove comments, these were related to problems I had with getting idba to run and are not related to A5.
* Make the assembly prefix a bash variable so that you would only have to change it in one place.

Thanks again.