Create `gotcloud archive ...` to record what was done

[pjvandehaar]

After we process data, we'd like for other people to be able to repeat our steps.

We need to record

• the commands that were run
• their arguments
• their versions

We could get this information:

• while running align.pl, umake.pl, and pipeline.pl.
• parsed out of the Makefile
  • Then just remove any lines starting with for, mkdir, etc.
  • How to figure out which targets we want, and in what order? Maybe use make --dry-run?
• parsed out of the Makefile's output
  • Not all pipelines prefix important commands with @, so this won't work.

We could get the versions:

• hard-coded because the programs are included in the repository
• by checking them
  • eg, to get the version of bwa, run bwa |& grep -Pio '(?<=version: ).+
  • This handles commands that are overridden in $PATH.

Alternatively, we could just write simple instructions and scripts for doing all of this manually.