From my understanding, mysql isn't compatible with Python 3. I've tried several methods on Google to downgrade my version of Python, like run
conda install python=2.7.12
But this didn't work. I specifically need to use mySQL as I'm trying to run RepeatModeler (bioinformatics tool) to analyze some genomic data. Can anyone help with this? I've been trying to solve this problem for awhile. Thanks!
You don't.
Python 2 and 3 are actually different languages/runtimes
If you call python it is python2, and if you need python 3 its python 3.
on ubuntu 18.04 for example
invoking python directly gives you
geek@heckate_router:~$ python
Python 2.7.15+ (default, Jul 9 2019, 16:51:35)
[GCC 7.4.0] on linux2
While python3
gives you
geek@heckate_router:~$ python3
Python 3.6.8 (default, Aug 20 2019, 17:12:48)
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
Basically python 2 and 3 can and do co-exist. Unless you need a specific version, in which case you may want something like virtualenv. Setting that up is some what out of the scope of my answer
As for mysql
Installing the mysql server metapackage installs the following packages
The following additional packages will be installed:
libcgi-fast-perl libcgi-pm-perl libevent-core-2.1-6 libfcgi-perl
libhtml-template-perl mysql-client-5.7 mysql-client-core-5.7
mysql-server-5.7 mysql-server-core-5.7
There's no requirement for python at all for it. There seem to be python and python 3 libraries for mysql ... but looking at repeatmodeler's github page, it seems perl based with no python prerequisites.
Practically you're looking at the problem the wrong way.
Interestingly that github page says
WARNING: There is a bioconda and a docker package floating around proporting to have a functional RepeatModeler package. Neither work correctly. For the time being we recommend installing this program as described below.
So the issue might be elsewhere - possibly with the anaconda repo you are using.
