# Using the system miniconda 3 install


# Using the system miniconda 3 install

I previously wrote about installing your own miniconda install 
[here](/posts/conda-tutorial) which I strongly suggest reading. However, after I
received many questions about getting the conda set up properly, I decided to
make the process of getting conda set up for you a bit easier.

I wrote a script that will:

1. Ensure you are not installing to your home directory.
2. Eliminate the need to download the miniconda installer.
3. Reduce the burden of getting the channels set up and the proper envs and pkgs
   settings in your `.condarc`
   
The script will also make sure you have write permissions to the particular
directory specified and won't make changes unless you approve. Lastly, you can
say that you'd prefer to run the commands yourself, and then copy/paste the 
commands into your own terminal.

## Running the script

I made a new miniconda3 install here:

`/local/cluster/miniconda3_base`

This miniconda install will have only ever have the base packages installed and
expects you to install any new conda packages in your own environments.

To get this conda setup for you to use, you can run this script:

`/local/cluster/miniconda3_base/init_miniconda3 <PATH TO DESIRED CONDA DIR>`

e.g.

`/local/cluster/miniconda3_base/init_miniconda3 /nfs4/core/home/davised/opt/conda`

This will generate the specified dir for you, if necessary, and then set up your
`~/.bashrc` to access the new conda bin.

The script will confirm that you actually want to run the listed commands before
running them. If you feel better about running the commands yourself, choose
option 2 (No) from the list, and feel free to copy/paste them individually into
your own terminal.

The script checks for your `~/.condarc` and backs it up, if desired. It also
lets you know if you have already cached environments in the `~/.conda` dir.

If the script is unable to generate the specified conda dir for you, it will not
make any changes and instead exit the script.

As an aside, if you've accidentally run the `conda init` command while in
`tcsh`, you may have experienced problems accessing your programs. Just delete
the `~/.tcshrc` file that conda made and you should be good to go. As a
reminder, we don't support running conda in `tcsh`, only `bash`.

Regardless of which shell you run `init_miniconda3` from, only your `~/.bashrc`
will be modified.

One reminder is to check out a node with `qrsh` when you want to build a new
conda env, or your conda command will killed after 2 minutes.

To use a conda env over `SGE_Batch`, add this to your shell script:

```bash
eval "$(conda shell.bash hook)"
conda activate <ENV_NAME>
...
[Insert commands from conda env here]
...
```

It also helps to run the `SGE_Batch` command while in `bash` instead of `tcsh` 
if you happen to have `tcsh` as your default shell.

## Final tips 

Use `mamba install` and `mamba create` as a stand-in replacements for the 
`conda install` and `conda create` commands. Here is a link to the
[mamba docs](https://mamba.readthedocs.io/en/latest/). `mamba` is faster and
will help resolve complex dependencies in a much shorter time than `conda` in
some cases.

Also, it's best practice to install all of your programs with a version number
specified, e.g. `mamba create -n python3.8 python=3.8`, and to specify all of
your programs when you create the environment so that all of the dependencies
can be resolved at creation time. Sometimes you can run into issues when
installing programs in different order after creation.

Please join the 
[CQLS BUG Slack](https://join.slack.com/t/osu-cqls-bug/shared_invite/zt-dbi8nff5-Ao22ZmZY6L3Ocr_a_zJB9w)
if you have additional questions regarding conda, and join the `#conda` channel.