Add use_conda_env param and Fix mysql command bugs

[rainoffallingstar]

1. Add use_conda_env params to use certain conda envs with bwtool installed.
2. Update mysql commands by adding "-A -P 3306" params for speed.

[PoisonAlien]

Hi,

what is the use_conda argument in this context? I guess it should be the environment name, but the main argument seems to be TRUE or FALSE.

[rainoffallingstar]

Hi!
Indeed, the use_conda argument should be designed to accept the name of the conda environment. It is not appropriate to simply name it use_conda, as this could potentially mislead users. I suggest renaming it to use_conda_env to avoid confusion and to clearly communicate the purpose of the argument.
I believe that bwtool is much easier to install via conda. I think this improvement would make this package more robust.

[PoisonAlien]

Has mysql been deprecated?

[rainoffallingstar]

I am using MariaDB on Arch Linux, and the mysql package is being deprecated. It is expected to be removed in a future release, and it's suggested to use mariadb instead. By the way, MariaDB is a fork of MySQL , which is originated from the same source but has better performents and easy to install.

[PoisonAlien]

I see. Thank you. Just FYI, there is a high possibility that the code base will be changed to use the RMySQL or the RMariaDB R packages instead of command line SQL queries.

[rainoffallingstar]

Aye, by the way, I've retained the original mysql command in a separate commit.

[PoisonAlien]

Yup. I will review them soon.

[PoisonAlien]

Again, use_conda shouldn't be the environment name instead of T/F.