Transfer code from Tools module of OrthoEvolution

[sdhutchins]

The tools module currently contains the below submodules.

Some of these modules may not need to be added to this package and are incomplete.

As it stands, the modules that currently need to be migrated are:

• ftp
• logit
• mygene
• otherutils (this may need to be added to just a utils module or something else)
• parallel
• sge
• streamieo

We may still like to hold onto pybasher, slackify, pandoc, send2server, and mpi as either scripts or add them to a utils file or some other kind of documentation to help people.

[grabear]

Some of the Tools modules can be deprecated:
Which ones? (list below)

• pandoc
• mpi
• streamieo (already deprecated via datasnakes/OrthoEvolution@7c61d53)
• sge (the pbs module replaces this in db_mana_update ) branch
• pybasher (in favor of https://github.com/liiight/notifiers as a dependency)

Some of the Tools modules need to be left in the package:
Which ones? (list below)

• mygene (move this to the top level)

Some of the Tools modules need to be moved to snakeutils:
Which ones? (list below)

master

• ftp
• logit
• parallel
• pbs

dev_master

• send2server

[grabear]

When developing this add all of the "for sure" sub-modules" to the master and create the package with that. All of the submodules that are still in the works, can be added after the fact to a dev-master branch or something.

[grabear]

This is just a thought, so let me know what you think @sdhutchins. I know we have a lot going on here, so what if we made separate packages for each of the submodules? (Please disregard the naming conventions, they are just placeholders for the concept) So we would have:

• snake-ftp (or snake-ncbiftp)
• snake-logit
• snake-parallel
• snake-pbs

And then if you wanted all of @datasnakes/snakes utilities you just install snakeutils. I feel like having them modular like this would be more appealing to people including other contributors.

I will, of course, have to finish my review of datasnakes/OrthoEvolution#155, but what are your thoughts on this?

[sdhutchins]

I actually think it's a solid idea tbh - and yes, also more appealing. It also will be probably easier for us to split them up and do things that way!

More than anything, snakeftp could just be snakencbi - I have some other stuff we could add there.

Maybe we could make logit and parallel into snakeutils and then snakepbs or even snakehpc or something as the 3rd one.

There's a lot of ways we could do it, but I definitely agree with splitting it into something more modular for people instead of a big-ish library.