Commit 61237fdb authored by peguerin's avatar peguerin
Browse files


parent cf42ba81
......@@ -44,16 +44,16 @@ Quickstart
1. open a shell
2. make a folder, name it yourself, I named it workdir
`mkdir workdir
cd workdir`
`mkdir workdir`
`cd workdir`
2. clone the project and switch to the main folder, it's your working directory
`git clone
cd snakemake_only_obitools`
`git clone`
`cd snakemake_only_obitools`
3. 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](
4. run the pipeline :
`bash /path/to/fastq_dat_files /path/to/reference_database_folder 16`
`bash /path/to/fastq_dat_files /path/to/reference_database_folder 16`
Order of arguments is important : 1) path to the folder which2) path to the folder which contains paired-end raw reads files and sample description file ; number of cores to assign (here for instance 16 cores)
5. run the pipeline step by step :
open the file `` to see details
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