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# File format #
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Metagenomics samples must be stored in a unique directory. Because there is a high variability in filename format, the difficulty to automatise paired-end data recognition increase. Filename are constrained and must respect the following format :
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<sample_name>(. | _)(r1 | R1 | r2 | R2)(fastq | fq | fastq.gz | fq.gz)
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exemple :
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S1.R1.fastq
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S1.R2.fastq
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S2_r1.fq
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S2_r2.fq
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*NOTE* : for now, fastq files must be uncompressed - I'm actually adding a rule for temporary decompressed files.
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# Installation #
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git clone git@gitlab.univ-nantes.fr:bird_pipeline_registry/genosysmics.git
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cd genosysmics
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(optional) conda create -n <project>
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(optional) conda activate <project>
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pip install .
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genosysmics init <path/to/dir/samples.fq> --wd <project_dir>
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genosysmics should be in your PATH, otherwise source your virtual environment.
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[Previous](Genosysmics)
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[Next](Usage)
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:warning: Here is the current installation method, but we are working on packaging the workflow so that it is directly available in Bioconda :warning:
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# Dependencies
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A working installation of **conda** and **git** is mandatory to build magneto. If you have **mamba** already install on your system, the creation of the main environment will be faster.
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* python 3.7+
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* python 2.7
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* snakemake 6.3.0
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* mamba 1.5.8
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* conda 4.10.3
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* click 8.01
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Other dependencies (such as python libraries for analysis, or to compute programs) are installed through the setup.py and conda management.\
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The default conda libraries management for snakemake is mamba, since a couple of month now. Even if it is possible to use conda instead of mamba for conda libraries management, the design of Magneto set mamba mandatory, as `--conda-frontend conda` does not propagate to the subworkflows.\
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Except if you use your own databases or already have downloaded them, MAGNETO will also require an internet connection.
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# Installation
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## Main conda environment installation
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Start by creating a conda environment containing snakemake, mamba and the python module click:
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```bash
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conda create -n magneto snakemake-minimal=6.3.0 click=8.01 mamba=1.5.8 -c bioconda -c conda-forge
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```
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> Note
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>
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> * If you have **mamba** or **micromamba** already installed, you can create the environment with it instead of conda.
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Then, activate your environment:
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```
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conda activate magneto
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```
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## Installation of magneto module in the conda environment
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Installation is performed using `pip`:
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```
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git clone https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto.git
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python3 -m pip install magneto/
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```
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**Magneto** is now installed in the "magneto" conda environment. Activate your environment whenever you need to run the pipeline !!
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[Previous - MAGNETO overview](https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto/-/wikis/Magneto)
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[Next - Usage](https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto/-/wikis/Usage)
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