Conda Tutorial

What exactly is Conda?

A package and environment manager
- Like apt/yum, but much more flexible
- Environments are isolated from each other
User-contributed package recipes
- Different “channels”, can create your own
- Updated constantly
Prebuilt binaries
- Linked to libraries in the same environment

Conda packages

Specific versions
Various sources ("channels")
Defined requirements
- Usually from the same or predefined other channels

Conda channels

conda-forge: Most dependencies (numpy, scipy, zlib, CRAN packages, etc.)
bioconda: Most bioinf packages (salmon, STAR, samtools, DESeq2, etc.)
defaults: Packages built by Anaconda Inc.
Order matters! Use this one:








$ conda config --show channels
channels:
- conda-forge
- bioconda
- defaults

$ conda config --prepend channels bioconda
$ conda config --prepend channels conda-forge

Finding Packages

Search https://anaconda.org
Use conda search














  $ conda search pysam
  Loading channels: done
  # Name                       Version           Build  Channel             
  [...]
  pysam                         0.16.0  py36h71d3148_1  bioconda            
  pysam                         0.16.0  py36h873a209_0  bioconda            
  pysam                         0.16.0  py37ha9a96c6_0  bioconda            
  pysam                         0.16.0  py37hc501bad_1  bioconda            
  pysam                       0.16.0.1  py27ha863e18_1  bioconda            
  pysam                       0.16.0.1  py36h4c34d4e_1  bioconda            
  pysam                       0.16.0.1  py36h71d3148_0  bioconda            
  pysam                       0.16.0.1  py37hc334e0b_1  bioconda            
  pysam                       0.16.0.1  py37hc501bad_0  bioconda            
  pysam                       0.16.0.1  py38hbdc2ae9_1  bioconda

Packages have versions, build numbers, build hashes/strings
- Build hashes include dependency information
Bioconda packages are also listed at http://bioconda.github.io/conda-package_index.html

Conda environments

A (mostly) self-contained directory with a set of compatible packages
Uses links to reduce disk space when possible
No more conflicting dependencies between versions!

common commands

conda info --envs (or conda env list)
- Lists available environments
```
```bash=
  $ conda info --envs
```
```
- You start in base
- The * indicates the active environment
conda create/conda env remove
- Create/remove environments
```
conda create --name=myenv python=3.8 numpy 'pysam>=0.16'
conda env remove --name=myenv
```
- Packages can have versions specified
- Min/max versions can be specified

conda activate/conda deactivate

Activates/deactivates an environment







command -v nanoplot
conda activate nanoplot
command -v nanoplot
conda deactivate
command -v nanoplot

conda install/conda remove

conda list






$ conda activate myenv
$ conda install snakemake
... a lot of status output ...
$ conda list
... many packages ...
$ conda remove snakemake

Keep your base env clean! (only the package manager + its deps)
Generously create/remove environments for different tools/workflows!

conda env export/conda env create

Exports or creates an environment from a YAML file













$ conda env export --no-builds > env.yaml
$ conda env create --name=more-map-and-call --file=env.yaml
$ head env.yaml
name: map-and-call
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1
- _openmp_mutex=4.5
- bcftools=1.10.2
- blis=0.7.0

Introducing `mamba`

Newer package manager called mamba
A reimplementation of conda
Compatible with conda
- Installed beside conda in the base environment
Much faster than conda

conda activate base
conda install mamba

from now: every time you see conda somewhere, replace it by mamba!

Sometimes it will complain, if so, you can always resort back to conda :)

Common pitfalls

Wrong channel order
Installing packages in your base env
Manually manipulating $PYTHONPATH
Avoid manually (i.e., not via conda/mamba) installed packages

Practicals

Practical 1

What are the most recent versions of samtools and Snakemake?

Practical 2

Let's create some new environments!

But first make sure that

conda is up to date

```bash=
$ conda activate base
$ conda update --all
$ conda --version

The correct channel order is in place

```bash=
$ conda config --show channels
channels:
    - conda-forge
    - bioconda
    - defaults
$ conda info
```

Practical 2.1

Create a new environment named "mapping" with bwa-mem2 and pysamstats
What versions of numpy and python got installed in it?

Practical 2.2

Create a new environment for Snakemake with mamba

Q&A

Questions?