ppcherng/squeezambler — pull request #1 by michaelbarton (2014-10-21 20:45:40+00:00)
Title: Refactor squeezambler image

Thanks for creating a squeezambler image Paul. You are very generous to
contriubute your time to towards this project. I have made some changes to the
image and this is quite a large pull request. Here is a summary of the main
points:

* The second arg ($2) pass to the Docker container is a fastq file rather
than a directory. I have therefore simplified the code to create the
INPUT_FILE for a single fastq as opposed to iterating over a directory.
This is the only required change to fit with the nucleotid.es API.

* I have switched the base operating system to use debian wheezy rather than
ubuntu. This saves around 100MB as the wheezy is smaller. I have installed
the additional required libraries. A smaller image size makes it simpler to
pull the image.

* I have built squeezambler from source. The reason is allow kmer values upto
128bp. Longer kmer values appear to have been very successful for velvet
and ABySS so I believe the same could be true for squeezambler. I have
added a careful proc entry to allow for longer kmer values and a higher
depth cutoff. This however increases the image size as I have to install
g++ and associated dependencies.