"could not find database dir: /db" despite providing one

sequenceserver
#1

Hi,

While trying out the docker version, I get this error despite providing a value, as below:

`
$ echo ${PWD}
/n/core/Bioinformatics/analysis/lmw/hox_in_lamprey/pmg1.d2

$ ls *.fa
hox_genes.c.fa hox_genes.fa hox_genes.sorted.fa scaffolds.fa

$ docker run --rm -itp 4567:4567 -v /path-to-database-dir:${PWD} wurmlab/sequenceserver
Could not find database dir: /db
`

I even tried creating /db and putting my fasta there but still get same behavior.

Any advice?

Thanks,

Malcolm

#2

Hi Malcolm,

The database directory, in this case the current working directory, should be on the left side of colon. And the right hand side should be /db.

docker run … -v ${PWD}:/db …

Regards,
Priyam

#3

Anurang,

Oops, my ignorance - thanks.

I am Getting another error now.

docker run --rm -itp 4567:4567 -v ${PWD}:/db wurmlab/sequenceserver:latest

Error response from daemon: Cannot start container c76ff26423a8d0bfdd271055ee78cb8c76880021b312263a34c910c9bb6da5bc: stat /n/core/Bioinformatics/analysis/lmw/hox_in_lamprey/pmg1.d2: permission denied

I had a working install of Docker but when I research the error I learn that Docker is no longer supported on CentOS 6.5 which is my OS.

Probably you’ll want me to upgrade my OS to get past this?

Or?

Thanks,

Malcolm

#4

Looks like a permission issue. You are running docker without root, in which case your user should be a part of docker group. Another thing to check is if SELinux policies are getting in the way.

Some info regarding docker on CentOS is here - https://github.com/wurmlab/oswitch#centos - could be a bit outdated.

Regards,
Priyam