update install and runtime deps, add bedops merge

[pdimens]

This PR does a few things:

1. fixes Use bedops instead of bedools merge for memory efficiency #68
2. fixes performance bottleneck #72
3. adds a bit more info to Spruce up readme #73
4. adds bedops installation to the install script
5. adds bedops version checking in `dDocent
6. prints the current version of software if installed version older than required version

Bumped version number to 2.9

[pdimens]

@jpuritz running the full pipeline (sans de novo assembly) on real data right now. I'll confirm if there are any issues.

[pdimens]

Can confirm the mapping and variant calling steps work as intended.

[jpuritz]

Thanks for working on this.  I should have some time next month to really take a look at things. Jon Puritz, PhD Assistant Professor Department of Biological Sciences University of Rhode Island 120 Flagg Road, Kingston, RI 02881 Webpage: MarineEvoEco.com Cell:    401-338-8739 Work:  401-874-9020 "The most valuable of all talents is that of never using two words when one will do. ” -Thomas Jefferson Sent via Superhuman ( ***@***.*** )

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On Thu, Apr 01, 2021 at 11:49 AM, Pavel V. Dimens < ***@***.*** > wrote: Can confirm the mapping and variant calling steps work as intended. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub ( #74 (comment) ) , or unsubscribe ( https://github.com/notifications/unsubscribe-auth/ABE5CR6B6FTGIJ4XYOG4EVLTGSIZBANCNFSM4YUAYBVA ).