...
...
...
...
...
...
...
...
...
...
We will now create a new CONDA environment to install the tools needed for mapping. The reason we need to create a new a new environments is because the QC and mapping tools have no compatible dependencies.
Create a conda environment called ONTvariants_mapping
...
| Code Block |
|---|
Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.12.0 latest version: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/barrero/miniconda3/envs/ONTvariant Proceed ([y]/n)? y Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate ONTvariants_mapping # # To deactivate an active environment, use # # $ conda deactivate |
...
Now we are done installing all the tools that we need for today.
...
Alternative approach to create a conda env and install tools (we are not doing this - this just for your information) - installing all tools at once (slower option!)
Prepare the following environment.yml file:
| Code Block |
|---|
name: ONTvariants_mapping channels: - conda-forge - defaults - bioconda dependencies: - samtools=1.20 - minimap=2-2.28 |
...
As you have seen, we can search at anaconda.org for other tools that we might be interested to use.
Remember, if you run into compatibility issues or errors, you can always create a new conda environment for the tool of interest. NOTE: you can switch between conda environements as follows:
| Code Block |
|---|
conda activate ONTvariants_QC ... ... ... conda deactivate conda activate ONTvariants_mapping ... ... ... |
...