blast-workqueue

Integrate WorkQueue with SequenceServer.

Currently it still require some modification on the SequenceServer code. Modify command method in lib/sequenceserver/blast/job.rb from:

@command ||= "#{method} -db '#{databases.map(&:name).join(' ')}'" \
             " -query '#{qfile}' #{options}"

to:

@command ||= "blast_workqueue \"#{method} -db '#{databases.map(&:name).join(' ')}'" \
             " -query '#{qfile}' #{options}\""

Frontend

Called for every single BLAST search:

Usage:

./blast_workqueue "blastn -db /var/db/est_human -query /tmp/query.fa -evalue 1e-5"

Backend

Constantly running, upon receiving msg from a frontend, create a WorkQueue task and dispatch it to work_queue_worker connect to the backend.

A password file can be used to authenticate between work_queue_worker and the backend.

Usage:

./blast_workqueue-backend
./blast_workqueue-backend --password <pwd-file>
./blast_workqueue-backend --unix-sock <unix-sock-path>
./blast_workqueue-backend --ip <ip-to-listen-on> --port <port>
./blast_workqueue-backend --help

Communication between Frontend and Backend

Commuication is done via socket, (support both unix socket and tcp socket).

Use Unix socket by default, with a path of "/var/www/sequenceserver/backend.server"

Current Limitation/Caveat

• The input cmd from frontend to backend and the output from backend to frontend are both as a file in /tmp, only the filename is send via socket, there is no clean up done by the frontend, so user or system need to clean up /tmp regularly. Plan to having the output send to frontend via socket.

• Currently there is no sanitizing done by this program, so any valid blast option will be passed as is to work_queue_worker for execution. If sanitization is required for your system, plz do so before calling the frontend.