Conda TP

Conda TP

Conda setup

How to access conda?

Conda is so used that it could even be installed by default to your
machine. To test this: conda --version
if not, may install it or got it by a docker image:

docker run -i -t -v ${PWD}:/data continuumio/miniconda3

on the IFB cluster, with modules: module load conda

Conda environment

We have already (blindly) use a conda configuration
file in the workflow session:
```
conda env create -n envfair -f envfair.yml
conda activate envfair
```

We will next detail the content of the configuration file, envfair.yml

Example of a conda configuration file

envfair.yml

channels:
  - conda-forge
  - bioconda
  - main
  - default
dependencies:
  - python=3.7.6 # specify python version (not required but can help with downstream conflicts)
  - snakemake-minimal=5.10.0 # workflow manager
  - graphviz=2.42.3 # for visualisation
  - xorg-libxrender
  - xorg-libxpm
  - wget=1.20.1 # for downloading files
  - fastqc=0.11.9 # for the RNAseq analysis
  - bowtie2=2.4.1
  - samtools=1.10
  - subread=2.0.1

How to access tools?

Manage Conda environment

create the working environment:
```
 conda create env -n myenv
```
activate it:
```
 conda activate myenv
```
if not yet done, install packages (specify the channel):
```
 conda install -c bioconda bowtie2
```
work with the tools
quite the environment:
```
 conda deactivate
```

1. Install Snakemake

Objective Create a conda configuration file to install the snakemake

tool.

Hint

Search its channel in the Anaconda cloud web pages
the “minimal” environment is sufficient

2. Install Snakemake

condaEnvSnakemake.yml

channels:
  - conda-forge
  - bioconda
  - main
dependencies:
  - snakemake-minimal=5.10.0

NOTE

It works with almost all markdown flavours (the below blank line matters).

run

conda create env -n condaEnvSnakemake -f condaEnvSnakemake.yml
conda activate condaEnvSnakemake
snakemake ...