Link executables into $admin_path/bin/ for cluster/workflow software management

make_admin_bin.sh

#!/bin/sh
set -u -e

admin_path=$1;

if [ -d "$admin_path/bin" ]; then
  mv "$admin_path/bin" "$admin_path/bin.bak"
fi

mkdir "$admin_path/bin"

# maxdepth of 3 will find
# software/rubygems-1.8.15/bin
# and
# software/rubygems-1.8.15/gems/bin
# but not e.g.
# software/rubygems-1.8.15/gems/gems/bundler-1.0.21/bin/
# which avoids duplicates

# will break if whitespace in path, but there should not be any
for bindir in $(find "$admin_path/software/" -maxdepth 3 -type d -name bin); do
    for binfile in $(find "$bindir" -type f); do
        ln -fs "$binfile" "$admin_path/bin";
    done;
done;

if [ -d "$admin_path/bin.bak" ]; then
    rm -r "$admin_path/bin.bak"
fi