Software package management with conda

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Cristian Riccio

1:36:56

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1 - Conda external resources

1 - Getting started with conda.html

2 - Data Camp resources for learning conda.html

2 - Anaconda installation and uninstallation

3 - Install Anaconda.html

4 - Install Anaconda using the Graphical User Interface.html

5 - Uninstall Anaconda.html

6 - Install Miniconda.html

3 - Introduction

1 - What is conda.html

2 - Find the version of your conda installation.html

7 - conda version or conda V find the version of your conda installation.html

8 - conda info get information on your conda installation.mp4

01:39

9 - conda package dependencies why are they important and how to find them.mp4

12:48

10 - Where are conda packages installed.html

4 - Search for conda packages

11 - Search for a conda package.mp4

01:43

12 - Search for a conda package on a specific operating system platform.mp4

12:00

13 - Search for a conda package on ALL channels at the same time.mp4

05:56

5 - Install conda packages

14 - conda install install a conda package.mp4

04:03

15 - conda install install several conda packages simultaneously.mp4

02:34

6 - Conda environments

3 - Which conda environment is currently active.html

16 - conda create create a conda environment.mp4

03:10

17 - Create a conda environment from a YAML file.html

18 - conda activate and conda deactivate activate and deactivate conda environments.mp4

03:02

19 - conda info envs list conda environments.mp4

01:50

20 - How do I find out which environment is currently active.mp4

04:39

21 - Install a conda package in the active environment.mp4

03:27

22 - Export a conda environment to a YAML file.html

7 - Uninstall a conda package or remove a conda environment

23 - conda env remove remove a conda environment.mp4

01:09

8 - Conda channels

24 - conda channels where conda packages live.mp4

08:02

25 - bioconda the conda channel for bioinformatics software.html

26 - List conda channels and their priorities.html

9 - Conda configuration

27 - condarc configure conda to add channels to be searched by default.mp4

04:54

10 - Conda package versions

28 - Find the version of a conda package in your active environment.html

29 - conda list REGEX find the version of conda packages using regular expressions.mp4

06:23

30 - conda list find the version of conda packages in a nonactive environment.mp4

04:25

31 - conda update update a conda package to its latest version.mp4

03:08

32 - To update conda to the newest version type the following in your terminal con.html

11 - Dependencies

4 - How does conda know the dependencies of a conda package.html

12 - Conda best practices

5 - Name environments reproducibly and informatively.html

33 - How to cleanly name conda environments reproducibly and with version numbers.mp4

07:53

34 - Exceptions to the rules for naming conda environments.mp4

04:11

35 - Speeding up the installation of conda packages.html

36 - Enable vim mode in Atom to speed up typing.html

Description

Use conda to install software, create separate software environment, delete software

What You'll Learn?

conda software package management
installing Anaconda
install software with conda
create separate conda environments
integrate conda with snakemake
control software versions with conda
learn about conda channels

Who is this for?

programmers

people new to programming

data scientists

biologists

bioinformaticians

people new to bioinformatics

software pipeline managers

science PhD students

What You Need to Know?

Basic Terminal/command line skills would be helpful

More details

Description
conda is a package management system. It forms part of the basic toolkit of any programmer. It is especially useful in bioinformatics and for people who use a lot of different software and packages. It is also useful for R and Python programmers. I would recommend that you learn it at the beginning of your programmer's or bioinformatician's career. It has saved me many headaches and has vastly simplified software installation. It is also indispensable if you want to use software which have incompatible dependencies. This happens very often. For example, some software want Python 2 on your system, while others want Python 3. conda allows you to solve this kind of problems.
Use conda to:
- find software
- find software specific to your operating system
- install software
- install R packages
- install Python modules
- install bioinformatics software from the bioconda channel
- create separate software environment
- delete software
- remove conda environments
- change conda environment
- control software versions
- update software versions
- use incompatible software on the same computer
- use the .condarc file to configure conda
- use conda efficiently by adding channels to the .condarc file
- write reproducible and tidy code
- name your conda environments in a tidy, informative and reproducible way
For the time being, this course does not teach how to package your own software into conda packages. You do not need this course to learn conda. However, I this course teaches you conda step by step with ample narration and explanations. As more students join, I will add more videos and improve the quality but for now all the topics above are covered.
Who this course is for:
programmers
people new to programming
data scientists
biologists
bioinformaticians
people new to bioinformatics
software pipeline managers
science PhD students

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Software Engineering

Cristian Riccio

Instructor's Courses

I studied biology at the University of Lausanne. That's where I learnt R and Python. I then started a PhD in genomics at the University of Cambridge, where I am currently applying bioinformatics methods to better understand the natural genetic diversity of the model nematode worm C. elegans. My expertise is in the development of reproducible bioinformatics workflows using snakemake.

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