Commit cd999371 authored by peguerin's avatar peguerin
Browse files

readme update

parent 7d8bdb32
......@@ -5,8 +5,6 @@ Only_obitools pipeline
1. [Introduction](#1-introduction)
2. [Installation](#2-installation)
1. [Requirements](#21-requirements)
2. [Optional components](#22-optional-components)
3. [Reporting bugs](#3-reporting-bugs)
4. [Running the pipeline](#4-running-the-pipeline)
......@@ -19,10 +17,6 @@ Here, we reproduce the bioinformatics pipeline used by [SPYGEN](http://www.spyge
# 2. Installation
You will need to install
## 2.1. Requirements
In order to run "only_obitools", you need a couple of programs. Most of
them should be available pre-compiled for your distribution. The
programs and libraries you absolutely need are:
......@@ -31,10 +25,6 @@ programs and libraries you absolutely need are:
- [GNU Parallel](https://www.gnu.org/software/parallel/)
## 2.2. Optional components
Other libraries are optional and only limit the features that are
built. These include:
# 3. Reporting bugs
......@@ -51,24 +41,19 @@ verbose as possible — e.g. include the command line, etc
* open a shell
* make a folder, name it yourself, I named it workdir
```
mkdir workdir
cd workdir
```
* clone the project and switch to the main folder, it's your working directory
```
git clone http://gitlab.mbb.univ-montp2.fr/edna/snakemake_only_obitools.git
git clone http://gitlab.mbb.univ-montp2.fr/edna/only_obitools.git
cd only_obitools
```
* define 2 folders :
- folder which contains reference database files. You can built a reference database by following the instructions [here](projet_builtdatabase).
- folder which contains pairend-end raw reads `.fastq.gz` files and the sample description `.dat` files. Raw reads files from the same pair must be named as `*_R1.fastq.gz` and `*_R2.fastq.gz` where wildcard `*` is the name of the sequencing run. The alphanumeric order of the names of sample description `.dat` files must be the same than the names of paired-end raw reads `.fastq.gz` files. The sample description file is a text file where each line describes one sample. Columns are separated by space or tab characters. Sample description file is described [here](https://pythonhosted.org/OBITools/scripts/ngsfilter.html).
* run the pipeline :
```
bash pipeline.sh /path/to/data /path/to/baseofreference
......
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