Go-Docker: a blast example - CeSGO Collaboration

Avec image simonalpha/ncbi-blast-docker

Sans montage

#!/bin/bash

# get the genome reference
curl -o Danio_rerio_genes_Zv9.fasta https://data-access.cesgo.org/index.php/s/1PRhWEtSK9v9wHD/download --insecure

# get the sequence to blast
curl -o sequences_COI.fasta https://data-access.cesgo.org/index.php/s/KdY6BCuC1KtvfBX/download --insecure

# create blastdb
mkdir blastdb
makeblastdb -in Danio_rerio_genes_Zv9.fasta -parse_seqids -dbtype nucl -out blastdb/zv9 -title "Zv9"

#run blast
blastn -query sequences_COI.fasta -task megablast -db blastdb/zv9 -outfmt 7 -out megablast.out

Avec montage home dir

#!/bin/bash

mkdir $GODOCKER_HOME/blast_test/

# get the genome reference
curl -o $GODOCKER_HOME/blast_test/Danio_rerio_genes_Zv9.fasta https://data-access.cesgo.org/index.php/s/1PRhWEtSK9v9wHD/download --insecure

# get the sequence to blast

curl -o $GODOCKER_HOME/blast_test/sequences_COI.fasta https://data-access.cesgo.org/index.php/s/KdY6BCuC1KtvfBX/download --insecure

# create blastdb

mkdir $GODOCKER_HOME/blast_test/blastdb

makeblastdb -in $GODOCKER_HOME/blast_test/Danio_rerio_genes_Zv9.fasta -parse_seqids -dbtype nucl -out $GODOCKER_HOME/blast_test/blastdb/zv9 -title "Zv9"

#run blast

blastn -query $GODOCKER_HOME/blast_test/sequences_COI.fasta -task megablast -db $GODOCKER_HOME/blast_test/blastdb/zv9 -outfmt 7 -out $GODOCKER_HOME/blast_test/megablast.out