To encapsulate the remote-fuser
application in a docker container so that it
can provide a FUSE containing BLAST databases to other containers.
remote-fuser
is a command line application from the NCBI SRA toolkit which
facilitates setting up FUSE on the local host. The BLAST database files
reside in the gs://blast-db
GCS bucket.
N.B.: these instructions assume Ubuntu Linux
make run
creates and runs a docker container with remote-fuser configured to get BLAST databases from GCS, however, these cannot be seen outside the containermake check
runs a few commands to demonstrate that.make run_shared
same asmake run
but it sets the bind-propagation to the value of theBP
environment variable (shared
by default).make stop
stops and removes the most recently started remote-fuser docker container.make clean
removes all binaries and locally downloaded scriptsmake fuse.xml
retrieves theremote-fuser
configuration file
-
Create a COS instance:
make cos_start
-
On the newly created instance (named
rmt-fuser-test-$USER
by default):git clone https://github.com/christiam/docker-rmt-fuser.git
-
Build image
cd docker-rmt-fuser && sudo bash -x cos-build.sh
-
Run the container
bash -x cos-run.sh
-
Check the local file system
bash -x cos-check.sh
-
Stop the container
docker rm -f rmt-fuser
-
Outside the COS instance, to stop it, please run:
make cos_stop