Commit b1f4d01c authored by peguerin's avatar peguerin
Browse files

set global variable

parent 8ae77263
#########################################################################
### set global variables
## species to process
#SPECIES=$1
SPECIES=mullus
#SPECIES=diplodus
## dDocent
CONTAINER=/entrepot/working/seaconnect/seaConnect--dDocent/seaconnect.simg
DDOCENT_CONFIG=/entrepot/working/seaconnect/seaConnect--dDocent/01-infos/ddocent_config.file
CONTAINER=/media/bigvol/eboulanger/seaconnect/seaconnect.simg
DDOCENT_CONFIG=/media/bigvol/eboulanger/seaconnect/01-infos/ddocent_config.file
#########################################################################
### RUN THE WORKFLOW
### create barcode files
bash 00-scripts barcodes.sh "${SPECIES}"
......@@ -25,16 +34,7 @@ bash 00-script/demort.sh "${SPECIES}"
bash 00-scripts/rename.sh "${SPECIES}" 01-infos/"${SPECIES}"_sample_information.tsv 98-metrics/"${SPECIES}"_samples_blacklist.txt
## dDocent
CONTAINER=/entrepot/working/seaconnect/seaConnect--dDocent/seaconnect.simg
DDOCENT_CONFIG=/entrepot/working/seaconnect/seaConnect--dDocent/01-infos/ddocent_config.file
CONTAINER=/media/bigvol/eboulanger/seaconnect/seaconnect.simg
DDOCENT_CONFIG=/media/bigvol/eboulanger/seaconnect/01-infos/ddocent_config.file
#### add a reference
#### add a reference genome fasta file to ddocent folder
ln -s /entrepot/donnees/genomes/"${SPECIES}"_genome.fasta 04-ddocent/"${SPECIES}"/reference.fasta
#### run the workflow "dDocent"
bash 00-scripts/ddocent.sh "${SPECIES}" "${CONTAINER}" "${DDOCENT_CONFIG}"
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment