Conda cheat sheet#

Conda cheat sheet

//
# Deactivating the activation of the base environment in Python:
conda config --set auto_activate_base false
//
**Listing all installed packages
conda list
# If you want to list all installed packages along its channels:
conda list --show-channel-urls
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#To install a package
conda install packagename
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# specifying multiple channels when installing a package
$ conda install scipy --channel conda-forge --channel bioconda
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# Install a package in the base environment
conda -n base packagename
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# Create a new environment with a set of packages
conda create -n foo instrain awscli samtools python=3.8

# update conda itself
conda update conda

#To install a certain package version
conda install <pkg>=<version>
e.g.:
conda install matplotlib=1.4.3

#To install a package from a certain channel
conda install -c bioconda pybedtools

#To uninstall (deinstall) a certain package
conda uninstall packagename

#We can upgrage packages:

conda update numpy

#Verify environment we are right now:
conda info --envs

#create a new environment with some packages installed
conda create --name bamqc numpy pandas

#activate the created environment
source activate bamqc

#deactivate the environment
conda deactivate

#installing a new environment with a new python version:
conda create --name blahblah python=2.7

#installing a new version with all python packages included in anaconda
conda create -n python2.7_env python=2.7 anaconda

#list all envs
conda env list

#remove a given env
conda env remove --name bamqc

#setting the environment variables for a specific environment:
#Read useful post:
http://www.benjaminmgross.com/conda-env-vars/

1)
$ echo $PATH
/home/benjaminmgross/anaconda/envs/my_env/

2)
$ cd PATH
$ mkdir -p ./etc/conda/activate.d
$ mkdir -p ./etc/conda/deactivate.d

3)
$ touch ./etc/conda/activate.d/env_vars.sh
$ touch ./etc/conda/deactivate.d/env_vars.sh

4)
./etc/conda/activate.d/env_vars.sh <File>

#!/bin/sh

export MY_KEY='secret-key-value'
export MY_FILE=/path/to/my/file/

5)
./etc/conda/deactivate.d/env_vars.sh <File>

#!/bin/sh

unset MY_KEY
unset MY_FILE

#activating table of contents in jupyter:
Install extensions from:
https://github.com/ipython-contrib/jupyter_contrib_nbextensions

#opening jupyter notebook on a particular working dir:
jupyter notebook --notebook-dir=/Users/yourname/folder1/folder2/

#Enter in the command mode (gray box with blue edges) and enter with ESC

# Select cells downwards:
shift+down_arrow

# Python markdown
This nbextension allows to display output generated by the kernel in Markdown cells

For example: If you set variable a in Python

a = 1.23
and write the following line in a markdown cell:

a is {{a}}
It will be displayed as:

a is 1.23
//
#save to a file all packages in an environment:
conda list --export > packages.env

#Then we can use this file to create a new environment:
$ conda create -n ch1env --file packages.env

//
*Saving an entire environment to a file:
conda env export --file env.yml
/
*Now, we can create the environment from the env.yml file:
conda env create -f environment.yml

//
#having info on the conda we have:
conda info
# especially important are the channels, because it conditions what programs are available
//
#adding bioconda channels
#The first one is optional and the order is important
(conda config --add channels r)
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

#Now we can install one the bioconda programs, like for example bwa:
conda install bwa
//
* Creating an environment from a yaml file:
conda env create -f environment.yml

And the contents of environment.yml is:
name: stats
dependencies:
  - python=3.4 
  - numpy
  - pandas

# create env with R and some certain basic packages
$ conda create -n r_env r-essentials r-base

# How do I prevent Conda from activating the base environment by default?
conda config --set auto_activate_base false
The first time you run it, it'll create a ./condarc in your home directory with that setting to override the default.

# How to activate the base environment if you chose not to activate conda's base environment in your current shell session
 eval "$(/homes/ernesto/miniconda3/bin/conda shell.bash hook)"

# Knowing all versions of a specific package
conda search -f <packagename>
 
# Knowing the active channels
conda config --show channels

# Knowing the channel urls for all installed packages:
 conda list --show-channel-urls