Commit f91649e3 authored by peguerin's avatar peguerin
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Update README.md

parent fe2b5a85
...@@ -42,33 +42,31 @@ verbose as possible — e.g. include the command line, etc ...@@ -42,33 +42,31 @@ verbose as possible — e.g. include the command line, etc
Quickstart Quickstart
1. open a shell * open a shell
2. make a folder, name it yourself, I named it workdir * make a folder, name it yourself, I named it workdir
``` ```
mkdir workdir mkdir workdir
cd workdir cd workdir
``` ```
* clone the project and switch to the main folder, it's your working directory
3. 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/snakemake_only_obitools.git
cd snakemake_only_obitools cd snakemake_only_obitools
``` ```
* define 2 folders :
4. 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 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). - 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).
- -
5. run the pipeline : * run the pipeline :
``` ```
bash main.sh /path/to/fastq_dat_files /path/to/reference_database_folder 16 bash main.sh /path/to/fastq_dat_files /path/to/reference_database_folder 16
``` ```
order of arguments is important : 1) path to the folder which contains paired-end raw reads files and sample description file 2) path to the folder which contains reference database files 3) number of available cores (here for instance 16 cores) order of arguments is important : 1) path to the folder which contains paired-end raw reads files and sample description file 2) path to the folder which contains reference database files 3) number of available cores (here for instance 16 cores)
6. run the pipeline step by step : * run the pipeline step by step :
open the file `main.sh` to see details open the file `main.sh` to see details
that's it ! The pipeline is running and crunching your data. Look for the log folder output folder after the pipeline is finished. that's it ! The pipeline is running and crunching your data. Look for the log folder output folder after the pipeline is finished.
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