README.md

Dockerized compound similarity scorers

A repositroy to hold the recipes used to make versions of compound comparison (alignment and scoring) codes that are no longer easy to install.

Possible wrappers to make more flexible

All of the Dockerfiles in this repo make images with the same setup - files specified on the commandline can be imported only from the present working directory. This is obviously an annoying limitation. A way of making some improvement (based on this blog is to put a short wrapper into the PATH which enables directory selection, see below (<IMAGETAG> identifies the image that the container to be wrapped will be launched from).

#!/bin/bash

# Check whether our first positional argument is a directory
if [[ -d "$1" ]]; then
    # It is a directory. Store the argument in a variable.
    dir_name="$1"
    # Remove the first argument from our list of arguments
    shift
else
    # It's not a directory, just use the current working directory
    dir_name="$(pwd)"
fi

# Run the container:
#     - in interactive mode
#     - remove it when finished
#     - mount a shared volume
# and then pass the rest of the arguments ("$@") to our container
docker run --rm -i -v "$dir_name":/share <IMAGETAG> "$@"