Commit 331f0cbb authored by Laure QUINTRIC's avatar Laure QUINTRIC
Browse files

add environment variable in extract.ini

parent b53c56c8
......@@ -44,14 +44,14 @@ Final output files are names :
* ABYSS_NAME_R2R.fastq.gz
## How to run ?
**extract.ini** : configuration file
**extract.ini** : configuration file to edit
* 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.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
```bash
./extract.sh
......
#Input parameters
[common]
#file containing primer definitions and selected barcode
properties = /home1/datahome/lquintri/abyss/abyss-dataref/properties.ini
properties = %(HOME)s/abyss/abyss-dataref/properties.ini
barcode = 18S-V1
#input directory with raw data
indir = /home1/datahome/lquintri/abyss/abyss-dataref/input/18S
indir = %(HOME)s/abyss/abyss-dataref/input/18S
#output directory with processed reads
output = /home1/datawork/lquintri/abyss/rawdataprocessing/18S
output = %(DATAWORK)s/abyss/rawdataprocessing/18S
#correspondance between genoscope and abyss names
samplename = /home/datawork-merlinabyss/1_Raw_Data/Sediment_and_Aboveground_Water/AbyssTest3/Correspondences_Codes_Genoscope_Abyss.csv
......@@ -43,7 +43,7 @@ if __name__ == '__main__':
configfile = handleArgs()
#parse config file
config = configparser.ConfigParser()
config = configparser.SafeConfigParser(os.environ)
config.read(configfile)
indir = config["common"]["indir"]
output = config["common"]["output"]
......
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