... | ... | @@ -4,30 +4,6 @@ The primary analysis is composed of the steps to go from the raw fastq files gen |
|
|
|
|
|
![fastq](uploads/9855695405d57446ffa0b7dc659ce0d3/fastq.png)
|
|
|
|
|
|
## Cloning the git repository
|
|
|
|
|
|
In order to use this analysis pipeline, you need to clone this repository. Note that this pipeline has been built to run on linux systems. It may not (probably will not) work on any other system.
|
|
|
To clone this repository, **you need a working install of git**:
|
|
|
|
|
|
```bash
|
|
|
git clone "https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline.git"
|
|
|
```
|
|
|
|
|
|
All locations of files described in this wiki page will be assumed to be relative to the main "srp-pipeline" folder.
|
|
|
|
|
|
## Creation of the conda virtual environment
|
|
|
|
|
|
All tools necessary for the pipeline to run are listed within a **conda environment** recipe located in "CONDA/rna.yml", hence **you need a working install of conda**. If you do not have conda, you can get it from either:
|
|
|
- the [miniconda](https://docs.conda.io/en/latest/miniconda.html) distribution
|
|
|
- the [anaconda](https://www.anaconda.com/distribution/) distribution
|
|
|
|
|
|
Due to the impossibility for conda to manage the dependencies of all the R packages needed, the conda environment is simplified to install only R and not the packages. All the R packages are installed after the conda environment by a R script, located in "CONDA/installDeEnv.R" via bioconductor.
|
|
|
You can manually run the creation of the conda environment, then run the R script to install R packages, or simply use the bash script "install_dependencies.sh":
|
|
|
|
|
|
```bash
|
|
|
./install_dependencies.sh
|
|
|
```
|
|
|
|
|
|
## Creation of the input files
|
|
|
|
|
|
In order to run the pipeline, you will need two things:
|
... | ... | |