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# Instalation

## install ocaml and opam

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You can check if you have `ocaml` and `opam` using
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```
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ocaml --version ##>= 4.11.1
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opam --version ## >= 2.0.2
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```

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### If you don't have `ocaml` and `opam`

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- pre install step
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```
sudo apt-get update
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sudo apt-get install m4 zlib1g-dev bubblewrap unzip
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```

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- install step
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install `ocaml` via `opam` according https://opam.ocaml.org/doc/Install.html

```
sh <(curl -sL https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh) # install opam
```

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- post install step
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```
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opam init --compiler=4.11.1
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eval "$(opam config env)"
```

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## install dependencies
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```
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opam pin add -y bistro --dev-repo
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opam pin add -y biotk https://github.com/pveber/biotk.git
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opam pin add -y bistro-bio https://github.com/pveber/bistro.git
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opam pin add -y phylogenetics https://github.com/biocaml/phylogenetics.git
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opam install -y ppx_csv_conv ocamlify utop
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```

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Some of these steps may fail because of missing packages (Blas,
gsl). `opam` will give hints in that case. After following them, just
execute the same command line.

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## install the pipeline and check if it works

```
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git clone https://gitlab.in2p3.fr/pveber/codepi.git
cd codepi
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make
make install
```

# Run the pipeline

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## First the test
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```
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make test
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```

## Second the analyse

```
make analyses
```