Mosquito short read alignment pipeline - dockerfiles

[JonKeatley112]

This PR adds a set of dockerfiles for the following programs

• BWA
• Samtools
• BioBamBam
• Picard

It also contains a README.md detailing their usage and how to build the versions needed for the mosquito short read alignment pipeline

Note GATK is provided by the Broad Institute via docker hub.

[alimanfoo]

Thanks so much @JonKeatley112 for this PR, LGTM (although I'm no docker expert so can't comment on the details).

Can I nominate @hardingnj and @gbggrant as reviewers, suggest merging once they both approve.

[alimanfoo]

Thanks @gbggrant.

@JonKeatley112 just checking in, are you planning to pin the versions of the alpine images you're building on?

@hardingnj any further comments here?

[JonKeatley112]

@alimanfoo Yes I was hoping to have them pinned already but will do so in the next hour or so

[gbggrant]

One other comment here. I wonder if we want to have the tools be installed in some standard directory (like /usr/) or is there such a standard? The current locations are:

/bwa/bwa /bin/samtools /root/picard.jar /usr/local/bin/bammarkduplicates

[hardingnj]

@hardingnj any further comments here? Looks good to me!

[JonKeatley112]

@hardingnj Just to check are you happy for me to merge?

[JonKeatley112]

One other comment here. I wonder if we want to have the tools be installed in some standard directory (like /usr/) or is there such a standard? The current locations are:

/bwa/bwa /bin/samtools /root/picard.jar /usr/local/bin/bammarkduplicates

This is an interesting idea, I keep flip-flopping on it. Everything executable gets added to $PATH so I am not sure what knowing its location gets you; Plus you can use which. But it is nice to have things standardised.

[alimanfoo]

Thanks @JonKeatley112 :+1: