Build Picard from source with htsjdk 4.3.0 for CRAM v3.1 support

[EddieLF]

Build the Picard image from source code rather than installing through the package manager. This allows us to explicitly build with htsjdk 4.3.0 which is required for compatibility with CRAM v3.1 (default CRAM version for samtools v1.22 onwards.)

Based on Devin McCabe's image from the Broad Institute:
broadinstitute/picard#2028 (comment)

Also adapts the entrypoint shell script from Bioconda and copies it into the image:
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/picard/picard.sh

Builds the image in two stages so that the build tools are discarded in the final image.

[github-actions]

🐳 Expected Tags

Some Dockerfiles have been modified in this PR. New tags are expected to be deployed.
The table below shows what the tags are expected to be on merging this PR.

Name	Tag
picard	3.4.0-2

[jmarshall]

FYI the debacle of HTSJDK 4.3.0 not having been properly released — and no corresponding Picard release having been made at all — was discussed again at yesterday's GA4GH file formats meeting. Various people are further stepping up their efforts to get this fixed and I'm hopeful that they will soon succeed and a more up-to-date Picard will appear in bioconda.

However at least in the meantime it's worth building it ourselves like this.

[jmarshall]

Because we use arguments like -Xms… that AIUI should be given to java itself, it would probably be better to use a script like bioconda's rather than just an alias.

[MattWellie]

YOLOO