Seqware command line needs a unzip option

[briandoconnor]

Use of docker necessitates people unzipping our bundles. We really should just migrate over to .tar or .tar.gz but, while we use a non-standard Zip64, we should really provide a simple command line util as part of the general command line. For example, here's what you have to do now:

java -cp seqware-distribution-1.1.0-alpha.6-full.jar net.sourceforge.seqware.pipeline.tools.UnZip --input-zip Workflow_Bundle_dockerHelloWorld_1.0-SNAPSHOT_SeqWare_1.1.0-rc.0.zip --output-dir  Workflow_Bundle_dockerHelloWorld_1.0-SNAPSHOT_SeqWare_1.1.0-rc.0

would really like something like.

seqware bundle unzip --input-zip Workflow_Bundle_dockerHelloWorld_1.0-SNAPSHOT_SeqWare_1.1.0-rc.0.zip --output-dir  Workflow_Bundle_dockerHelloWorld_1.0-SNAPSHOT_SeqWare_1.1.0-rc.0

[denis-yuen]

An additional thought, Java 7 now offers Zip64 out of the box. https://blogs.oracle.com/xuemingshen/entry/zip64_support_for_4g_zipfile

What we can do is switch to a standard zip64 bundle for 1.2 (while deprecating the old zip64 format for 1.1.X) so that standard Linux tools will work out of the box for unzipping bundles (We should still add an unzip command though for consistency).