A base image with curl and gosu installed, intended for multi-stage builds where curl is later dropped.
A base image with curl and gosu installed, intended for multi-stage builds where curl is later dropped.
A base image with curl and gosu installed, intended for multi-stage builds where curl is later dropped.
This is a Docker image of a vanilla iRODS 4.2.7 server that works out of the box. To be used for running tests only.
This is a Docker image of a vanilla iRODS >=4.2.11 server that works out of the box. To be used for running tests only.
The server version may be chosen by passing the Docker build argument
--build-arg IRODS_VERSION=<version> (default is 4.3.0).
A makefile is supplied that will by default build all images and add
metadata to them based on git describe.
cd ./docker
make
Each container that provides command line programs is self-documenting and is able to install its own proxy wrappers outside of the container, to allow these programs to be run transparently.
The images include the singularity-wrapper tool which allows programs to be listed and their wrappers installed. The install target should be set to a volume mounted into the container and the -p (install prefix) option of the tool set accordingly. The -h option will show online help.
e.g. Show online help:
$ docker run wsinpg/ub-18.04-irods-clients-4.2.11:latest \
singularity-wrapper -h
e.g. List the programs provided by a container:
$ docker run wsinpg/ub-18.04-irods-clients-4.2.11:latest \
singularity-wrapper list
baton-chmod
...
samtools
e.g. Install wrappers to $PREFIX/bin:
$ docker run -v $PREFIX:/mnt/tmp \
wsinpg/ub-18.04-irods-clients-4.2.11:latest \
singularity-wrapper -p /mnt/tmp install
$ ls $PREFIX/bin
-rwxr-xr-x 1 kdj staff 406 Apr 12 15:47 baton-chmod
...
-rwxr-xr-x 1 kdj staff 409 Apr 12 15:47 samtools
The release contains irods 4.2.7 clients bundled from
ub-16.04-irods-clients-4.2.7 to be used on ONT machines, where we
cannot run containers. Given the complexity of the iRODS clients'
dependency chain, the location of the plugins must be provided in the
iRODS environment file using the irods_plugins_home key. Some
dependencies for these plugins must also be preloaded to avoid local
system libraries from being pulled in, e.g.:
$ LD_PRELOAD=path/libarchive.so.16:path/libcrypto.so.1.0.0:path/libssl.so.1.0.0:path/libxml2.so.2:path/libicuuc.so.55:path/libicudata.so.55 \
./exodus/bin/iinit
A script to do this is set up by the ansible used to set up the instruments (https://gitlab.internal.sanger.ac.uk/npg/oxford_nanopore_instruments).
Keith James kdj@sanger.ac.uk