Commit 39785cb1 authored by peguerin's avatar peguerin
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Update README.md

parent 053ae27a
......@@ -43,12 +43,14 @@ verbose as possible — e.g. include the command line, etc
Quickstart
1. open a shell
2. make a folder, name it yourself, I named it workdir
2. make a folder, name it yourself, I named it workdir
```
mkdir workdir
cd workdir
```
2. 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
cd snakemake_only_obitools
......@@ -57,6 +59,7 @@ cd snakemake_only_obitools
- 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).
4. run the pipeline :
```
bash main.sh /path/to/fastq_dat_files /path/to/reference_database_folder 16
```
......
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