Current

Documentation is on the Wiki of the web site

BioMAJ in 5 minutes with Docker

You can get a running BioMAJ instance running with Docker in 5 minutes

docker pull genouest/biomaj
docker pull mongo
docker run --name biomaj-mongodb -d mongo
# Wait ~10 seconds for mongo to initialize
# Create a local directory where databases will be permanently stored
# *local_path*
docker run --rm -v local_path:/var/lib/biomaj --link biomaj-mongodb:biomaj-mongodb osallou/biomaj --help
Copy your bank properties in directory local_path/conf and post-processes (if any) in local_path/process

Sample bank for testing

Copy in local_path/conf/alu.properties

[GENERAL]

######################
### Initialization ###

db.fullname="alu.n : alu repeat element. alu.a : translation of alu.n repeats"
db.name=alu
db.type=nucleic_protein

offline.dir.name=biomaj/ncbi/blast/alu_tmp
dir.version=ncbi/blast/alu

frequency.update=0

### Synchronization ###

files.num.threads=1

# NCBI (download fasta)
protocol=ftp
server=ftp.ncbi.nih.gov
remote.dir=/blast/db/FASTA/

release.file=
release.regexp=
release.file.compressed=

remote.files=^alu.*\.gz$

#Uncomment if you don't want to extract the data files.
#no.extract=true

local.files=^alu\.(a|n).*


docker run --rm -v local_path:/var/lib/biomaj --link biomaj-mongodb:biomaj-mongodb osallou/biomaj --update --bank alu

docker run --rm -v local_path:/var/lib/biomaj --link biomaj-mongodb:biomaj-mongodb osallou/biomaj --status

Biomaj v1