Commit 93869a86 authored by Laure QUINTRIC's avatar Laure QUINTRIC
Browse files

modify way of running pipe

parent 1397d101
......@@ -45,16 +45,17 @@ Final output files are names :
## How to run ?
**extract.ini** : configuration file to edit
* DIRECTORY : current directory of pipeline
* INPUT : path to the input directory containing the fastq.gz reads files of one marker for several samples.
* OUTPUT : path to output directory
* PROPERTIES : path to file containing forward and reverse primers for different markers
* BARCODE : name of the marker (ie : 18S-V1) (this marker must be listed in the PROPERTIES file)
* SAMPLENAME : path to the csv file containing abyss and genoscope sample names
**extract.sh** : script which will run extract.py on the configuration file **extract.ini**. Each samples (and its two "paired-end" files) will be parse separately. For each sample, the job **extract.pbs** will be run on 2 cores and 10gb of memory. This can be changed by editing the header of extract.pbs
**extract.pbs** : script which will run extract.py on the configuration file **extract.ini**. Each samples (and its two "paired-end" files) will be parse separately.
```bash
./extract.sh
qsub extract.pbs
```
(c) 2018 - Ifremer
......
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