Benrwong: conda environment sharing

2019-03-29T21:20:54Z

conda environment sharing

← Older revision		Revision as of 21:20, 29 March 2019
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	(oepython3) [<username>@n-9-34 ~]$ '''conda deactivate'''		(oepython3) [<username>@n-9-34 ~]$ '''conda deactivate'''
	[<username>@n-9-34 ~]$		[<username>@n-9-34 ~]$

			===Sharing Conda Environments===

			If you run into a coworker whose using a conda environment and you would like the same environment, ask your coworker to export the environment into a YAML file.
			$ conda env export > environment.yml

			The user who wants to use that environment file will create a new environment with the YAML file as an argument
			$ conda env create -f environment.yml

Benrwong: how to install miniconda/conda and activate conda environments

2018-10-16T22:18:56Z

how to install miniconda/conda and activate conda environments

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Get miniconda shell script from anaconda/continuum
[username@n-9-34 ~]$ '''wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh'''
--2018-10-16 14:52:55-- https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.continuum.io... 104.16.18.10, 104.16.19.10, 2400:cb00:2048:1::6810:130a, ...
Connecting to repo.continuum.io|104.16.18.10|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 62574861 (60M) [application/x-sh]
Saving to: “Miniconda3-latest-Linux-x86_64.sh”
100%[======================================>] 62,574,861 107M/s in 0.6s
2018-10-16 14:52:55 (107 MB/s) - “Miniconda3-latest-Linux-x86_64.sh” saved [62574861/62574861]

Run miniconda3 installer
[username@n-9-34 ~]$ '''bash Miniconda3-latest-Linux-x86_64.sh'''
Welcome to Miniconda3 4.5.11
...
(follow wizard steps and miniconda3 will be installed)
Do you accept the license terms? [yes|no]
[no] >>> '''yes'''
Miniconda3 will now be installed into this location:
/nfs/home/<username>/miniconda3
- Press ENTER to confirm the location
- Press CTRL-C to abort the installation
- Or specify a different location below
[/nfs/home/<username>/miniconda3] >>> '''/nfs/home/<username>/miniconda3'''
Do you wish the installer to prepend the Miniconda3 install location
to PATH in your /nfs/home/<username>/.bashrc ? [yes|no]
[no] >>> '''yes'''
.
.
.
Thank you for installing Miniconda3!

Log out then log back in OR run shell so your shell (bash or csh/tcsh) will be aware of the newly installed conda commands.

Create a new conda environment with packages of your choosing. In this example, I will create an openeye python3 environment with relevant packages.
$ conda create --name <environment name> <additional packages to install in environment>

$ '''conda create --name oepython3 python=3'''
Solving environment: done
.
.
.
Proceed ([y]/n)? y
.
.
.
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

List your conda environments. See that the environment you just created is there.

[username@n-9-34 ~]$ '''conda info --envs'''
# conda environments:
#
base * /nfs/home/<username>/miniconda3
oepython3 /nfs/home/<username>/miniconda3/envs/oepython3

Activate your conda environment to customize it or work with it. I will be adjusting my openeye environment.

[<username>@n-9-34 ~]$ '''source activate oepython3'''
(oepython3) [<username>@n-9-34 ~]$

If you don't need your conda environment anymore. Deactivate it.
(oepython3) [<username>@n-9-34 ~]$ '''conda deactivate'''
[<username>@n-9-34 ~]$

Install Miniconda - Revision history

Benrwong: conda environment sharing

Benrwong: how to install miniconda/conda and activate conda environments