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----
-title: "Managing your software environment"
-subtitle: "Tools for Reproducible Research NBIS course"
-output:
-  xaringan::moon_reader:
-      self-contained: true
-      seal: false
-      css: ["default", "../template.css"]
-      nature:
-          slideNumberFormat: ""
-
----
-
-layout: true
-<div class="scilife-logo"></div>
-<div class="nbis-logo"></div>
-
----
-
-class: center, middle
-
-*Managing software environments with*
-
-<img src="https://upload.wikimedia.org/wikipedia/commons/thumb/e/ea/Conda_logo.svg/2056px-Conda_logo.svg.png" style="width:50%;padding: 15px 15px 15px 15px;">
-
----
-
-class: center, middle
-
-<img src="r-reproducibility-6-638_cropped.jpg" style="width:75%;padding: 15px 15px 15px 15px;">
-
-Full reproducibility requires the possibility to recreate the system that was originally used to generate the results.
-
----
-
-# Conda is a package, dependency, and environment manager
-
---
-
-.green[Package]: any type of program (_e.g._ bowtie2, snakemake etc.)
-
---
-
-.green[Dependency]: other software required by a package
-
---
-
-.green[Environment]: a distinct collection of packages
-
---
-
-<br>
-.center[Conda keeps track of the dependencies between packages in each environment]
-
----
-
-# Conda channels
-
-.green[Channels] are remote directories containing packages.
-
---
-
-<br>
-Two common examples are
-
-
-- .green[bioconda]: a channel specializing in bioinformatics software
-
-- .green[conda-forge]: a community-led channel made up of thousands of contributors
-
----
-
-# Conda, Anaconda, Miniconda, Mamba...
-
---
-
-- .green[Conda]: the package manager itself, written in python
-
---
-
-- .green[Mamba]: a faster reimplementation of Conda (written in C++)
-
---
-
-- .green[Anaconda]:
-  - an installer for conda containing over 7,500 open-source packages
-  - a cloud service where conda packages are hosted ([anaconda.org](https://anaconda.org))
-  - a distribution of packages for data science ([anaconda.com](https://anaconda.com))
-
---
-
-- .green[Miniconda]: an installer for conda containing only the most necessary packages to get started
-
---
-
-- .green[Mambaforge]: installer with Mamba in the base environment, pre-configured for conda-forge channel
-
----
-
-# Mamba vs. Conda
-
-<img src="https://mamba.readthedocs.io/en/latest/_static/logo.png" style="width:25%;padding: 15px 15px 15px 15px;">
-
-In short: Mamba is a faster implementation of conda.
-
-- Install mamba with conda: `conda install mamba -n base -c conda-forge`
-
-or see the [documentation](https://mamba.readthedocs.io/en/latest/installation.html) for how to do a fresh install.
-
-- Simply replace `conda` with `mamba` on the command line:
-
-```bash
-mamba env create --name project_a -f environment.yml
-mamba env update -f environment.yml
-mamba env export > environment-full.yml
-mamba env export --from-history > environment-history.yml
-```
-
----
-
-# Defining and sharing environments
-
-
-Define a Conda environment in an `environment.yml` file:
-
-```yaml
-channels:
-  - conda-forge
-  - bioconda
-dependencies:
-  - fastqc=0.11
-  - sra-tools=2.8
-  - snakemake=4.3.0
-  - multiqc=1.3
-  - bowtie2=2.3
-  - samtools=1.6
-  - htseq=0.9
-  - graphviz=2.38.0
-```
-
---
-
-```bash
-# Create a new environment from YAML
-$ conda env create --name project_a -f environment.yml
-```
-
---
-
-```bash
-# Update an existing environment from YAML
-$ conda env update -f environment.yml
-```
-
---
-
-```bash
-# Export existing environment as new YAML file (including all dependencies)
-$ conda env export > environment-full.yml
-```
-
---
-
-```bash
-# Export historical environment, i.e. packages listed in the original YAML
-$ conda env export --from-history > environment-history.yml
-```
-
----
-
-class: center, middle
-
-# Questions?