edirect_docker

Dockerizations for Entrez Programming Utilities (a.k.a. edirect)

Description

This repo exists to support dockerizations (e.g. Dockerfiles) that allow users to run edirect. Currently, you can run edirect v18.6.. either using a Biocontainers-compatible image with the file at ./biocontainers/, or using a more compact minimal image with the file located at ./minimal/.

Tutorial:

This section describes how to set up new Docker images with the provided Dockerfiles, and how to get started with using edirect from the images. You will need access to a terminal with Docker installed in order to run the docker commands below.

Clone the `edirect_docker` repo

You can clone the main GitHub repo with the image Dockerfile, using:

git clone https://github.com/metamaden/edirect_docker

Build Docker images

Build a Docker image using docker build <location>. This will run an appropriately named file called Dockerfile that should be available and readable from the specified <location>. In this repo, two Dockerfiles have been provided: one using the Biocontainers environment as its base; and one using just the minimal dependencies for Entrez Utilities. The former has added convenience if you're running other Biocontainers images, but the latter is smaller and quicker to install.

Build the Biocontainers-compatible Docker image from the cloned Dockerfile, setting the --tag argument to some informative name:

docker build edirect_docker/biocontainers/ --tag edirect-biocontainers:latest

Build the minimal image with:

docker build edirect_docker/minimal/ --tag edirect-minimal:latest

View information about the final images with docker image ls, which should return something like:

(base) root@User-PC:/mnt/c/Users/User/Documents/GitHub/edirect_docker# docker image ls
REPOSITORY              TAG       IMAGE ID       CREATED          SIZE
edirect-biocontainers   latest    53efcb0ee109   3 minutes ago    1.12GB
edirect-minimal         latest    cdea17e223f4   8 minutes ago    136MB

Notice the Biocontainers image is a little over 1Gb, whereas the minimal image is just 136Mb.

Example `edirect` queries

You can now pass a query to the Docker image in one line like so, replacing < IMAGE_NAME > with either "edirect-biocontainers" or "edirect-minimal":

docker run -it < IMAGE_NAME > esearch -db gds -query 'GPL13534[ACCN] AND gse[ETYP] AND Homo sapiens[ORGN]'

You could also run queries from an interactive session, like so:

sudo docker run -it < IMAGE_NAME > bash # run interactive session
esearch -db gds -query 'GPL13534[ACCN] AND gse[ETYP] AND Homo sapiens[ORGN]' # try a new query

Either of the above queries should return something like the following:

<ENTREZ_DIRECT>
  <Db>gds</Db>
  <WebEnv>MCID_63b33b4784d8ee4a3124bbff</WebEnv>
  <QueryKey>1</QueryKey>
  <Count>1594</Count>
  <Step>1</Step>
</ENTREZ_DIRECT>

Troubleshooting

OpenSSL

I encountered an error involving OpenSSL which was fixed when I updated my base image and edirect to their latest versions. Actually, this error inspired this post to make sure others can run a dockerized edirect error-free. Note that some existing Dockerfiles (e.g. here) use static versions for their base image (e.g. FROM biocontainers/biocontainers:v1.0.0_cv4). By changing this to FROM biocontainers/biocontainers:latest we can ensure the latest version of the base image is always installed.

The latest version of edirect can be found at its FTP address (ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/). This needs to be updated in the Dockerfile, which you can do manually or which can feasibly be scripted as a version check in the Dockerfile. The lines in question are:

ENV ZIP=edirect-< LATEST_VERSION >.tar.gz
ENV URL=ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/< LATEST_VERSION >/

Works cited

The Dockerfiles in this repo are based on the file at https://github.com/BioContainers/containers/blob/master/entrez-direct/7.50.20171103/Dockerfile.

metamaden/edirect_docker