README.md

# Instalation

## install ocaml and opam

You can check if you have `ocaml` and `opam` using

```
ocaml --version ##>= 4.11.1
opam --version ## >= 2.0.2
```

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

- pre install step

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

- install step

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
```

- post install step

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

## install dependencies

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

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.

## install the pipeline and check if it works

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

# Run the pipeline

## First the test

```
make test
```

## Second the analyse

```
make analyses
```